Yes, well, we already saw how humanity approaches that question, now haven't we? "They could to it," is insufficient. The Soviets could have done it. But they didn't, and we didn't launch a preemptive strike, either. The same logic applies.
2. We would have absolutely no idea how they think.
By the posits we have so far, we have significant expectation of being able to know how they think decades before either end has the capability to visit destruction - radio contact comes decades before interplanetary rocketry.
Earth like does not mean supporting human life.
"Earth like" in this context generally means having a solid, rocky surface, liquid water available (which implies an atmosphere, though it's content may be open to discussion), and a mass such that humans can manage to live there is some measure of health. I assert that if we cannot live largely unprotected on each others' worlds, there's really no reason to fight. At least, not before we both have technology to mine asteroids.
Their physiology might differ so much that we couldn't even enter their buildings.
Well, that's nothing - we can always put up new buildings - we usually do when we move into new territory, you know.
And just because there is a flora & fauna on the planet doesn't mean that we are compatible with that. Its even unlikely that we can breath the air even when it includes oxygen.
You are correct that the wrong balance of gases would be problematic. It isn't enough to have Oxygen, Nitrogen, and CO2, but we need them in right concentrations to keep breathing (and presumably, so would they). And we are unlikely to match their biology - we can't eat each others' food, and so on.
That planet certainly was earth like and yet all the plants, animals and even the atmosphere was a obstacle and not helpful at all.
Yes. To the point where, if not for "unobtanium", humans wouldn't have bothered with the planet at all. So, if it is so hostile, why blow them up? The fact that they *could* blow you up isn't itself a threat, unless they have *reason* to.