So specifically I have a question about CoS, but I'm thinking about the issue more generally, which is:

The book states that Father Lucian mentions the threat of the loss of St. Andral's bones to the characters if they have a good aligned cleric or paladin. My players have neither. I have 3 evil players and a LG dwarf barbarian. (If you don't know CoS, suffice it to say that the bones protect the priest and his church, and the bones have been stolen)

So- what to do? They'll never find out about the bones, unless they manage to get to the coffin maker's shop and break in.

And if they never get the bones, the church gets attacked and the priest killed. I was kind of hoping to use him because he seems like the single priest in the entire valley that's not crazy. So he could be useful if we needed to resurrect a player or something.

What to do about this? Let it go- too bad, so sad, my players picked evil alignment so they don't save the priest? Or use my discretion to push them towards the coffin maker's shop and breaking in there? How do you approach a situation like this, generally? Let the story lead to where it leads? I'm inclined to trust in the story structure and stick to it. If the priest dies, well... most of my players chose evil alignments. With great evil comes great irresponsibility, so they say. Or something like that.

Anyway, I sound like I know what to do, I reckon, but I'm afraid of painting myself into a corner. A live, sane, good priest could come in handy for my players.

Thanks.

How evil are they?  If Ireena would vouch for them, the priest would take them into his confidence.  Also, he might tell Ireena and she might tell the players on their own.

You could also treat the block to be suggesting the information is told voluntarily to the players if they have a good alignment. 

As they are evil, the information is not volunteered freely. Instead, they may notice the priest acting nervous, and evasive about the problem if confronted. A few successful skill checks or an evening spying on him as he prays for the strength to find the bones later, he begrudgingly gives up the information.

5e has no "know alignment" spell. Detect good and evil does not give any information on PC alignment. The fact is that Father Lucian has no way to know the alignment of anyone entering the church. Even the Hallow spell doesn't work on alignment.

However, most of your party is evil. If they are playing evil then they may have no interest in helping the church defend against Strahd. I hope that the characters have some good reason to be in Barovia and fighting against Strahd, otherwise what is the point of the module for them? You may have already got the players to come up with some reasons for their characters to be working together, to be acting as a group, working as a team and why they would choose to oppose Strahd. Any of these reasons could motivate them to be nice to Father Lucian.

Anyway, since Lucian has no way to tell alignment, he would have to base any request on character behaviour. If the characters act like murder hobos, do obviously evil things then he won't trust them to help against Strahd which will likely lead to the desecration of the church by the vampire spawn - however, if you want to keep the NPC around you could have him survive after the church is burned to the ground and the congregation hurt during the attack.

Quote from TimCurtin >>

How evil are they?  If Ireena would vouch for them, the priest would take them into his confidence.  Also, he might tell Ireena and she might tell the players on their own.

 This.

Even an evil character might see a value in making things good with Ireena, and SHE might see some good in making sure the church doesn't fall.

Agree with the others that you don't necessarily need to follow the script about Father Lucian only asking a good-aligned cleric and/or paladin for assistance. Despite most of the party being evil, Father Lucian might still request their assistance if their actions and/or behaviors demonstrate their ability to perform goodness in this dark land. Or, as some of the others suggested, you might have another NPC vouch for them based on previous "good deed" accomplishments.

And, with that being said, you also don't have to have Father Lucian die if you move forward with the church being attacked. If it benefits your campagin to let him live, then you just say that he survives. Perhaps Strahd's minions attack and destroy the unprotected church, but Father Lucian escapes the assault or is badly (versus fatally) wounded. The group loses the potential safety and sanctuary of the church if it's destroyed, but Father Lucian can recover and provide some clerical help after he recovers.

Quote from Javier_Phenergan >>

Agree with the others that you don't necessarily need to follow the script about Father Lucian only asking a good-aligned cleric and/or paladin for assistance. Despite most of the party being evil, Father Lucian might still request their assistance if their actions and/or behaviors demonstrate their ability to perform goodness in this dark land.

Depends a lot on how you define "evil" too as part of the alignment grid.

An evil character is, I read, generally interested in self advancement over that of "the common good" or "the community".  A lawful evil person doesn't go around murdering people and smashing things; they're the sort who manipulate systems to their own benefit and ideally in a way that no one really realizes how much it's to their own end.  An "evil" character could still very much take stances that benefit others, just as long as they also get a more than fair compensation.  

In other words:  The text should probably read that Father Lucian would ask assistance of anyone they believe will truly work to find the bones for the community and not simply take them for themselves.

Presumably the way Father Lucian detects 'good-aligned cleric or paladin' is by such cues as looking at their holy symbol.

Quote from Pantagruel666 >>

Presumably the way Father Lucian detects 'good-aligned cleric or paladin' is by such cues as looking at their holy symbol.

 Perhaps, but considering there are many realms from which creatures can reach Barovia, Father Lucian would need knowledge of the pantheons from several different universes in order to identify them all.

In addition, there are many dieties that could potentially have good, neutral or even evil worshippers. A neutral god of war like Tempus may well have Good, Neutral and Evil followers. A war cleric of tempus could be any of these alignments.

Finally, paladins draw their power from their oaths and may not have a diety at all.

So, although Father Lucian could try to figure out the alignment of a cleric or possibly a paladin based on the symbols they carry ... it might not work out at all.