MWSE could probably do that, but it would only be a fix for player-made mods that use the MWSE version of the function. I doubt they would include it, since a player who knows the issue could just use the replace-gem scripting by adding a few lines of code.
This also might be something the Morrowind Code Patch could do, but again it is fixable another way.
The point of both MWSE and MCP is to do something that can't be done any other way, which is not the case with the soulgem issue.
Well, Stupor had posted a question to the effect of trying to see if there was a way to fix the problem in one place, globally, so that it becomes 'automagically fixed' for every script, without requiring every script to individually implement a solution. The only way I can see that you could accomplish that, specifically (that is, a one-fix-for-all) would be to replace the built-in RemoveSoulGem function, something that only MWSE or MCP could do. If they could do that, that would likely fix the 'official' quests as well.
In software engineering, if you can fix a problem in one single place, so that client code of the function (in this case, scripts) don't have to implement a fix every place the function is used, that is the *best* solution, because it A) fixes the problem everywhere at once, with the least effort, and B) eliminates the possibility of client-code error (such as in this case where the modder didn't realize the need to implement the check-and-restore code).
The only reason I suggested the solution I did is because, at the moment, it appears to be the only solution, even though it is really an ugly hack. The *better* way to solve the problem would be to fix the RemoveSoulGem function, but I'm not sure that's possible, even for the MCP or MWSE guys.