Wells are only useful for wounded, and to make dwarves happy. Why a well filled with water makes them happy is beyond me...
The goblins should leave. However, advanced DF players often have a fuck-the-world lever for such situations. I suggest reading boatmurdered if the concept is new to you.
General defense suggestions. Never, unless you know better, meet them in combat. Let them come to you. Every proper mountain hall has a defensive cooridor for bloodbaths. Its usually a good idea to have a contingency in case that fails. I have emergency doors for quick lock-downs and a draw bridge before and after my defensive cooridor. The fortress proper starts beyond that.
Its often a good idea to have underground "bunkers" that aren't connected to your fortress for the occasional straggler to hide in. There are tons of ways to make them safe, often abusing ramp position in relation to doors and hatches works well. Its not uncommon to have pillboxes employ a similar idea, that are connected to your fortress, and not accessible from the outside, for marksdwarves, dragons, or captured FB's with a ranged attack.
Also, in general train more marksdwarves. If they aren't effective you don't have enough of them. Even unskilled marksdwarves, en mass, are deadly and its a "safe" defense. Not to mention they can take pot-shots at goblins stopped at the gates. Might even be able to injure them enough to reclaim the surface.