*Brushing up on my Melnibonean*
If you don't get a "The thread of prophecy has been severed...." message then the person(s) you killed is fair game as far as the main quest goes. It IS possible to kill secondary quests by killing someone, but you may never know unless you play through the game again.
The glass weapons aren't rare, but they certainly aren't common early in the game either...use 'em if you can until you find better

. There is one special piece of armor in Ebonhart, but I wouldn't worry too much about the stuff on the altar (just remember who you sell it to in case you need to buy it back at some point).
S_S