Do "forgiven" felonies still count towards the ending?
Solution 1:
According to a few posts in this thread, paying double the usual Mana cost to "Reincarnate to Atone" will remove the effects of felonies on the ending:
And as long as you reincarnate to atone for sins before you finish the game, you can still get the good ending. A special reincarnation erases those felonies for double mana cost: you lose the boost in assembly and discount at the shop, but keep the EXP multiplier.
You can get all the felonies you want on them. As long as you do the special reincarnation before you beat the game, then you'll be all set.