The only reasons I can imagine for it being wrong are consequentialist ones (i.e., the wrongness resides in the consequences such acceptances produce), and they strike me as weak reasons at that. First. the acceptance might encourage illegal or immoral activity, by creating a demand or outlet for such activity. Second, the acceptance could be interpreted by some as an endorsement of the activity -- drug or arms dealing, gambling, prostitution, etc. But you'd have to show (1) that the acceptance really is being interpreted as endorsement, and (2) that the perceived endorsement is causing something bad to happen.

Now, in Mother Teresa's case, I'd have to say these reasons don't hold. Both of them constitute what Mother Teresa would have considered the serious sin of scandal, and I doubt that she would have willingly committed it. Most university administrations don't share those sensibilities, so whether (1) or (2) is a danger is something to consider.

Perhaps, though, I'm overlooking some features that would make accepting money from certain sources morally wrong. I'd be interested to hear what other panelists think.