According to the TF2 wikithe TF2 wiki, a fully charged sniper round does three times the damage of an uncharged sniper round. Therefore, if you can get off three shots in the time it would take to charge, then you should go with (2). However, keep in mind that you're going to use a lot more ammo this way, and that gradual damage is often easier for the Engineer to repair than a series of more damaging shots.
Changed the link to official tf2 wiki, from the poorly maintained unofficial one.