Any sort of meaningful "fix" for her heart would likely have to happen near the very end, or even in an epilogue. The disaster and emotional roller coaster of facing no solutions to her problem are what elicit everyone's passionate interest in this character, why throw that out? The writers nailed it, don't take that experience away. Make it an inevitable choice everyone has to live through, this content is too rich and fits the tragedy I believe the writers were going for, last minute or not. The reason so many people have grown attached to Karlach is yes, the journey along the way, but the reality of her condition takes it to another level, don't reject this! This is critical.
Wouldn't you rather feel profoundly elated realizing that the doom you were set up for were met by say, Dammon with a crew of Gondians by his side showing up on the docks end scene? Having it be him instead of Wyll or a variation of the two that says "No Karlach, you don't have to do this, we found a way to fix you!" Wouldn't that open the door to a more rewarding conclusion than finding a fix somewhere in early to mid act 3? Missing out on the hope that kills? The reward of a solution needs a suitable climax, Karlach deserves this in respect to her already established position, her writing.
Of course choosing returning to Avernus over allowing Dammon and the Gondians to replace her heart immediately would have to have it's perks. Something along the lines of Karlach has greatly diminished capabilities with the new engine or the recovery isn't a guarantee and she may he handicapped in some way, there is an unknown future unless they had more time to come up with a solid design. Karlach would have to go from Barbarian level 12 to civilian level 3. Installing a temporary new engine to stay in Faerun while they perfect the design also incurs the higher likelihood of the transplant exploding and killing everyone in the attempt. So repeat attempts come with high risk. Make the choice a heavy and impactful one, do you let emotions running high override the logical long-term solution for an immediate solution to avoid Avernus? Or continue the adventure with peace of mind knowing there is something actively being worked on to fix the engine once and for all.
Her going to Avernus may be the time they need to come up with a perfect new engine, in the the meantime she's rocking the Doom soundtrack casually dismembering pit fiends for fun with her legendaries rather than just hamstringing them . While Tav and Wyll are casually one-rounding Raphael level encounters with whatever build they're running. Razing the hells with Zariel trembling in fear, to quote Wither's cut epilogue voice files.
Remember Karlach is the type for adventure and living a physically engaging life, she lives for combat and excitement, even if she has a house in Balder's Gate, she will definitely be taking up mercenary work or adventuring with Tav taking on hill giants or tracking down devils, fiends, etc.
What I think people are asking for and they don't know it, is keep the emotions running high, keep the hope that kills theme until the very end, but make it complicated and rewarding.
Edit: Also a good way for Karlach to address any unfinished business in Avernus, that is her style after all. Some check-list items crossed off.
