One of my players wants to play a Warlock of the Undying that is a spirit possessing the body of another but doesn't realize it. I'm totally fine with that part. I want to make the body of the player character the phylactery for the lich he serves. So long as he keeps killing and absorbing souls, he can continue to earn the patron's blessing. 

Is this too much to subject a player to?

If you're playing an Evil adventure, it's just fine. If you're playing a Heroic adventure then you're setting the player up for a very difficult time, if not failure. You're giving the player carte blanche to kill anything and everything simply to remain a player character. If you have anyone in the party who is hunting undead, a paladin, or otherwise able to recognize the evils that this character will be about...then it will facilitate in party conflict. It's a very risky road to walk as a DM.

Yeah, that was my worry. My plan was to have it be something that could be discovered and then allow to research various methods of transferring themselves to another body or something. My other thought was to make the phylactery their pact weapon. That seems somehow worse though since they have mechanically built their character around their weapon. 

If you're attached to the idea then I'd take it as more of a character arc rather than a mechanic of the character. Start off with small things that indicate the coming calamity:

Rats seem to gather in places the character spends long times in. Passing through a town may not reveal this, but if they spend a couple days there the rat population seems to grow.
Carrion feeders are seen more often when travelling, buzzards and the like will pass over head more often.

Eventually there is a bit of a miasma around the character. Those who spend time near the character will smell something that's not quite right, such as grave dirt. As time goes on it becomes more potent.

Continue to add more effects that start to show the Patron's origin. Becoming secretive and fascinated with death and eternal life could become ticks that the character gains. 

I think you should get the players buy in if you want to put his class powers in danger in the future base on the patron relationship. If the player is into it, awesome! If not, please reconsider.

If the player is not on board you can always have the body be the phylacty anyway, and reveal at some point that each  time he kills it feed the lich, and let them just deal with that fact (so many possible plot arcs), without taking away their class abilities when they don't kill.

In 5th edition no class abilities are tied to a code of behavior (rules as written), not cleric, paladin, or warlock. I see a lot of people want to add restrictions from previous editions to these classes, which is fine, but talk to your players first.

Thanks I was looking for more of a narrative beat. 

Quote from Mael >>

I think you should get the players buy in if you want to put his class powers in danger in the future base on the patron relationship. If the player is into it, awesome! If not, please reconsider.

If the player is not on board you can always have the body be the phylacty anyway, and reveal at some point that each  time he kills it feed the lich, and let them just deal with that fact (so many possible plot arcs), without taking away their class abilities when they don't kill.

In 5th edition no class abilities are tied to a code of behavior (rules as written), not cleric, paladin, or warlock. I see a lot of people want to add restrictions from previous editions to these classes, which is fine, but talk to your players first.

Thanks for the advice. I am a big fan of being straight with my players on anything involving their character. She asked me to create some pretty staunch terms to the pact her character is not aware of.