I wouldn't be too sure about an inability to interact. Given what we know about the fundamental laws of chemistry, it's entirely possible that the formation of life as we know it may be the only real way life can form. I wouldn't be too surprised if we discovered microbes that look and function very similarly to our own viruses and bacteria, etc., including DNA/RNA or some very closely similar molecule and mechanism.

But overall I agree with you. There are likely to be many differences, and even if they were exactly like Earth microbes the chances of them bothering us or us bothering them would be just as unlikely as a chimpanzee catching a cold from an iguana.

I think it much more likely that they could be biological irritants or even toxins, if indeed they affect us at all.

I think the main concern is that we'd want to study them as isolated lifeforms, and any Earth proteins or other contaminants would greatly hinder such studies. Even if we could clearly separate out the contaminants, we couldn't be certain if the Martian organisms had reacted to the Earth substances in some way.