It's just an unfortunate turn of events - you can do that section at low levels, 2-3 I'd suggest, but usually better to arrive on your own terms ;-) I'd just reload and talk your way in (or sneak in - there are alternate routes and you don't need to pick the lock on main door near beach, or even talk to the people topside. Picking lock is an option with high dex character and thieves tools). If you arrived in a bad way, out of resources and overrun, then unless you're lucky you'll have to redo it. But as long as you are level 2 or so, should be doable (don't go in guns blazing, use some stealth to set up first).
