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.
I don't think Archer's actions are depicted as the right ones - in fact, it's shown countless times the morale dilemma that he faces when he makes the actions, and touches on this in season 4 when he's all emo about space exploration to Hernandez.
And I know Star Trek is about human morales and their ingenuity and etcetcetc, but it can get kind of grinding to show humanity as this almost nigh-wrong dogooders of the galaxy on a constant basis. Most of Star Trek wanted to show humans in a good light, their possibilities. Season 3 of Ent wanted to show humans at their lowest, and the choices made during that, which can show a more believable side to any sentient life; regardless of how great they think their values are, there is a threshold to it.
Archer and the crew did go into the Expanse with the intention of guns blazing, as evidenced when Trip is all in Archer's grill about not pussy-footing around when it came time. But in the end they did manage to settle their differences, regardless of how it came about, and ended in the happy, diplomatic, Star-Trek-style ending. So I don't particularly see the problem.
Honestly, if you were in Archer's shoes, how would you have handled the whole saving-the-humans mission?
"Excuse me, you stole a lot of my cargo, can I have it back?"
"Oh ok. :-)"
"I need your warp coil otherwise my entire planet will be destroyed and a couple billion people will be dead!"
"Well you can't have it."
"That's okay, thanks anyway. :-)"
Also, if you really don't like the un-utopian view of humanity during season 3, a small arc in season 4 might not be to your taste either, as that also shows a portion of humans being baaaaad.