I can certainly see this happening considering what you're getting here is the "Scion exclusive version" and once the promotion goes away good luck finding it again on the PSN in order to download again in the future. In order to avoid 'losing' the game I suggest you use the Vita content manager to copy M:RC over to your PS3 for storage purposes whenever you feel the need to free space on your Vita memory card.
I don't think that'll be the case this time around. If you go back even further to 2008 or 2009, Rag Doll Kung Fu: Fists of Plastic was free for a limited time, it was a promotion with Sprint. About 4 years later that game is still on my purchase history. Decent, mindless, party fighting game, btw.
I think that we should all be ok simply by "purchasing" it on the ps store. If you're tight on space or hate having those install bubbles on you're xmb you will most likely have access to it in the future.