The big difference in this case is that we have tacit (or maybe even explicit) consent from the Yemeni government to hunt Al Qaeda. So the representatives of the people of that country are allowing us to kill these people basically on their behalf. (which doesn't make it OK, but is a major differnce)
It's not just that we are bullying Yemen into allowing us to bomb people in their country - it's that the Yemini authorities (and probably most of the population) don't want these people operating in their country but they lack the resources and infrastructure to stop them themselves; and that's where we come in.
Bare in min that we also give Yemen a lot of military aid so that we DON'T HAVE TO come in and do their law enforcement for them. In this case that wasn't sufficient and we intervene on their behalf
To make your example comparable you would need to have a person that is evading US authorities, operating in the US, and that we are completely incapable of stopping (and only some other country could do it for us?)