What comes to justification of release in those days. I would imagine there could have been two unique factors at that point.
1. The thought that the games lifespan would be longer than usual, as that game was one of the first releases and not too many releases were coming for that machine. This can somewhat been even seen as having happened, since if i correctly remember, they were including Marble Madness with sold A500s still in beginning of 90s (this is just a feeling based memory, not a real checked fact). And hence this would mean that as long as number of machines would increase, so would sales of the game increase.
2. I also wonder if their calculations were partially based upon the thought that Amigas would sell fast enough, that at point the game would become budget game (supposing they already had realised games had three lifes of full price, middle price and budget price - and actually Marble had fourth life as bundled with Amigas), there would already be enough Amigas sold that they could perhaps even make same amount of profit as they made when they launched it for full price still.
and in addition in Electronic Arts case:
3. Electronic Arts decided to want to support Amiga. At that point EA was still not only about money, but about ideals, and they or someone had decided Amiga was the way they wanted computers to go, and hence they were supporting in ways they could, even if it wouldnt make much sense always.
I could also imagine that they also could have figured, that even if it would make them negative balance at beginning, they could anyway take their space as major player in Amiga market, and when that market grows bigger, they would still be able to keep that lion share, instead of starting from zero market share, like some others did.
I can also imagine that part of the reason why Marble Madness was in Commodore Bundles for so long was because of EAs dedication to Amiga at beginning. That might have partially been a thank you from Commodore to them. That maybe they had two different games to think about, and both were equally good, but other one was EA and otherone was something else, hence, due to past support, EA won the bundle place.