The problem is, I don't believe for an instant that this was their only course of action - or would have been if Archer's previous poor decisions hadn't led up to it. He never tried to negotiate with the Xindi, which would have been the logical course of action in the first place. His stopping their weapon would have only bought them some time, but you know they would just build another one. When he was told by the time traveler that he could stop them from bombing earth, I don't think they meant by force. After all, he did have only one ship that was seriously outnumbered and outgunned. But that was the only tactic he had tried so far.
It wasn't until Daniels stepped in again (his role in the plot often seems contrived according to what direction the writers want the story to go) in "Azati Prime" with that Xindi artifact and told him how to explain to the Xindi that they'd been duped that Archer even thought about just *talking* to them. But by then it was too late because he had already been captured by the reptilians. It came off as an act of desperation, not a negotiation for a peace treaty.
I kind of like the Xindi. They have a unique culture where 5 sentient species had all evolved on the same planet. They had their squabbles, but they had made it work where each had an equal voice in the coucil dedicated to their well being. This kind of unity shows that they have passed one of the tests for admittance into the Federation. They've been tricked into believing humans are a threat, and are acting in self-defense. So how is it necessary for Enterprise to see them as arch-enemies that need to be stopped at all costs? They need to have their information corrected, that is all. But Archer is proving them right - that humans are ruthless.
But this series has drastically reduced it's moral values to get to this point. Star Trek has always been about bringing out the best in humanity, but this is not an example of that. Archer's crew are more a reflection of how modern people (specifically Americans) perceive "problem solving" when it comes to threats. It doesn't show what we can be, it only reflects how we are now. There is a real "end justifies the means" attitude presented, since the hurtful actions Archer takes are presented as the "right" decisions for the circumstance. This is taking a low road for Star Trek, and I'm disappointed in it.
What you're not taking into account is this is a prequel to TOS. There was no Prime Directive, No Federation. Earth was infants in Space Exploration, and the Vulcans showed us over and over again, they didn't believe Earth was ready to be out there, being cowboys. This arc of Archer's, is what made the way for the Federation see in TOS and later in TNG. Look at the difference between TOS and TNG Federation, you have that same difference between ENT and TOS.
Yes, absolutely, Archer and crew were out of their League, it was Earth's first venture out there, and their first experience with an Interstellar threat, and they made a lot of mistakes (which in turn taught Kirk and Picard and all those who came after not to make those same mistakes). ENT is, what, almost 200 years earlier than TNG?
In Voyager, even Capt. Janeway makes a comment about how "uncivilized" Kirk's Federation was, and that he'd be drummed out of Starfleet of her day. Naturally, 80 some years before Kirk, it's going to be even more uneven on the scale of good to bad decisions.