ToA is essentially an end of the world scenario type adventure. Someone needs to succeed or Acerak will bring a new god into existence which will probably continue to feed on the souls of the dead and will probably be even harder to destroy. Of course, its in your game world and you can respin it however you like.

In terms of having another group deal with it. It doesn't need to be sequential with the current group. I played through this and my party succeeded but there were several points in the module that indicated that other groups were also trying to accomplish the same task. There are the remains of other adventuring groups around, there are the Red Wizards and there could be whomever else you want to put into the module. If this group can't succeed then perhaps there is another group right behind them or even ahead of them (in terms of time) that may have already completed some aspects of the adventure. If you want new characters to play it out they could even run into the current characters who have survived and are trying to escape.

However, a party of three will find this a challenge even if they are far over the appropriate level (unless you tone things down). The Yuan-ti could be very difficult depending on how the encounters go and whether a diplomatic solution is found. The tomb itself contains a lot of deadly traps and your party may have a lot of trouble with that aspect (we had a rogue with the observant feat and expertise in stealth, perception, investigation and thieves tools which made finding, understanding and avoiding or disarming traps relatively painless) ... without that character the tomb can get very nasty just wandering around never mind dealing with some of the occupants ... and the odds of dealing with the soul monger, the atropal and Acerak at the end are also very low unless they are significantly toned down as well.