Either you're smart enough to understand the concept of consent or you aren't. Even if there is a sliding scale of intelligence of creatures (I have some issues with the concept of intelligence as a thing that can reasonably be objectively measured, but we can put that aside for now), whether you're intelligent enough to understand what you will be doing and what will be done to you and make an informed decision about whether you want to do it seems a pretty binary thing, and largely independent of your intelligence in other contexts (e.g. ability to use tools).

You could make the argument that alien sex might be complicated enough for whatever reason that that the aliens would argue that humans couldn't meaningfully understand everything that was being done to them and thus could not, by definition, give informed consent, but at least from my experience, humans seem pretty on board with things they don't fully understand. Whether it's ethical to fuck someone who has admitted that they don't know anything about what you're going to do to them, is aware they may be harmed by it, and wants to do it anyway is another question.

Besides, all we'd need is for one human to fuck one alien for science to know whether or not it was safe.