This isn't a simple 'disagreement' with the government. We're talking about someone taking refuge in a foreign country (this is a key detail), where we really have no power to do anything, to actively plan and execute attacks against the United States and its allies (either here, or abroad).
Anything we do, without the permission of the host country, to apprehend this individual, is potentially an act of war. In that scope, sending a Hellfire missile against this guy, should he prove to actually be a terrorist, is probably a little less aggressive than sending troops into harms way.
If we sent troops in to 'arrest' the guy, what then? What happens when he fights back? We'll have dead people on the ground. What happens when the host country's military responds trapping our soldiers? That's a diplomatic headache, to put it mildly. Do they shoot their way out? Surrender to be tried and imprisoned? Do we let the host country try to arrest and extradite? We've seen how well that works with Pakistan - their intelligence service leaks like a sieve, warning the targets before troops get into position...
What do you propose to stop this individual?
Seems simple, if the host government is allowing terrorists to openly plan and coordinate attacks on its soil, they have given up any pretense of being a legitimate regime, and should be replaced.
