I can't see how it could become problematic. By creating a company or product template all it does is allow a company to say "we support the WMF", while knowing full well that they can't lie due the beady eyes and open edit policy around here. It allows them an easy way to take from the advertising account rather than the feeble donation account. It also gives their PR/advertising teams a reason to take interactive stuff more seriously than they do with the overrated and costly broadcast media.
I can't see many companies paying just to get a "we support the WMF" notice on the article about them. What I thought you were suggesting was removing the logos from all company articles unless they pay us - that's a very different thing, and completely fails NPOV, which is one of our most important policies.