What has tended to do for the various New-Labour ministers during their time (Mandleson, Blunkett et al) has not been so much the 'offence' that they have committed, but the incessant attempts to weasel out of it afterwards.
In Hain's case, it is the use of the 'fake' think tank to channel money in that is causing him the problems, rather than the not declaring it. Even if it is above board, it certainly smells fishy, so we need him to be up front about what was going on and what he knew about it.
And if it turns out that he was using it as a dodgy way to circumvent the rules, then he probably will have to go...