I think they will be fully capable of measuring intelligence, absolutely. We are certainly capable of noting the difference in intelligence between an elephant and a lizard, so I am sure they'll be far more capable than we are of evaluating our level of intelligence.
But I am trying to see things from the perspective of these creatures that are far more intelligent than we are. If they are enough more intelligent, they won't think there is that much difference between a giraffe and humans. It all depends on how much more intelligent than us they are.
I believe they will have to be so much more intellegent than we are that they will consider the difference between us and a giraffe inconsequential. From our perspective, that is outrageous. I think they will find our outrage amusing, pat us on our heads and then proceed to dissect us.
Let me put it this way: Suppose we use some measure, we'll call it the Universal Intelligence Scale or UIS, to gauge intelligence. Suppose giraffes average 25, dogs and cats 35, elephants and dolphins 60 and humans 100. I believe space travelling aliens would measure something like 1000 or more on such a scale. The difference between them and us will entirely outpace the difference between us and giraffes.
There might be some 'specialist' from among their population that thinks we're interesting at some point. What that specialist does to us in order to study us depends on alot of things, but I doubt they'll be considering whether or not we'll be harmed in the process.
So, yes, they'll be capable of recognizing intelligent life, and to them, we just won't even be in the running.