I don't agree. The Doctor was sentient, so any relationship between sentient consenting adults is ok with him, at least in theory. It's a slippery slope as to at what point a hologram is considered a person. I thought that whole topic was interesting in Voyager.
By the later seasons the Doctor did have feelings for Seven, so he was capable of desire at least. Kes always saw the Doctor as a person, so that aspect wouldn't be an issue, although it's questionable if her feelings for him would or could have become romantic. I'd think at least initally he'd have been stuck in the friend zone, as he was with Seven, but that could've been interesting too.
I liked Seven with the Doctor a heck of a lot better than Chakotay anyways, that was just awkward and bad. A real taint on the ending.