Someone being more affected doesn't mean that the crime or action itself is less bad. If someone was raped, but it didn't seem to bother them, does that mean that it's ok? What if, for example, a child was molested, but they grew up without any psychological problems and were self admittedly unaffected? Does that mean that it was ok that they were molested? In a court of law, at least in my country, damages can vary depending on the suffrage of the victim. Someone may be awarded more or less based on how they were affected. Morally, however, it's always just as bad. It's great if the victim is able to move on, but I'm still disgusted by the act of rape itself.

We can't communicate effectively with animals, no, but in this case specifically I think it's fairly safe to say the animal was straight up raped. If the animal is whimpering, bleeding, ran away after... I mean, does it matter if the animal was able to actually say the word "no"? You wouldn't see that and think the animal was not consenting? What if it was a person who didn't speak your language, would you assume in that circumstance that it was alright to go ahead with sex under those conditions?

OP said the man was charged with rape, so I assumed it was rape. Even if the dog miraculously was unaffected and seemed willing at the time, humans and animals are not built the same. A human penis entering a dogs orrifus (I'm assuming it was either anally or vaginally) would do a lot of damage. Even with the trauma of rape aside, surely it would count as abuse anyhow?

It's not like we only have a set amount of empathy to give. If it was really really bad, or just bad, shouldn't you just feel bad anyway? I think it's quite evil to discount that animals suffering because you don't think it was bad enough.