That's fair enough, my concern was that Beth would slap it's name on the older Fallout boxes which could confuse consumers into thinking they made those games, which would be unfair on Interplay.
IMO just keep the old series in it's trilogy box, and whatever Beth makes from Fallout 3 onwards, keep it seperate.
Occasionally people mistaken a game's publisher for its developer, particularly when the developer is not well known (and if Interplay isn't in this category yet they're getting there). Over the years we've certainly seen it here when people credit games to Bethesda when they only published them. You can still see it today over in the WET forums.
However, anyone who really cares that much about who made the game will be able to figure it out pretty quickly. I also doubt that Bethesda's logo would appear during the start up unless the current collection publisher (which isn't Interplay) already does this.
As I mentioned earlier, no one credits 2K Games for Oblivion even though they helped with distribution and Bethesda would be filling a similar role for the Fallout collection if the publishing rights were passed to them. If this happens there will be a few people who are confused, but most people are going to figure the situation out pretty quickly, I really don't think you need to worry.