This is an old problem in shmups. The Gradius series in particular is infamous for how the player is left weak and defenseless after loosing a life, since you get most of your firepower from the options you earn and they are lost when you die. The way it was solved in Gradius V was that after you die, you get a chance to collect them back immediately. I haven't actually played the game myself, so I can't comment on the details. I imagine they float in space for a while before disappearing for good. Another way would be to let them float slowly away and the player have to hunt them down, creating a risk/reward situation.
Giving the player a few well chosen power-up's at key points, like you suggest, is another method that is used. It's a really tricky one to balance correctly though, since you might end up making the game to easy. The player will exploit any mechanic you give them. This method has always felt like a last resort measure from the developers to me. Like they realised they hadn't got the balance correct in the first place and had to do something to at least save the game somewhat.
The first method is more based on skill and will form an organic part of the game. The downside is of course that inexperienced players will still end up with inadequate firepower.