Well if the malware messes with network settings, you might not be able to even remote into it... Or if you have to boot into Safe Mode to remove components, you'd have to do Safe Mode with Networking - and some remote desktop apps may not work in Safe Mode.
I mean, it really depends on the infection in question.
I've done it several times over remote desktop with people's systems - but it was nothing more than a simple Trojan that didn't take me long to remove.