No, you are not damaging anything that way, and, after all, what would be un-natural about the cocked hammer position?
When dismounting the lock, the first thing taken off is the mainspring. If you have an 1879 tool, just slip it over the cocked mainspring and let the hammer down easily. The captured spring will wiggle right off of the plate and stirrup, and may be put aside for reassembly. It is actually handy to have several M1879 tools - they're cheap and very useful. And, they don't slip, as a mainspring vice sometimes does. The only time a mainspring vice is actually required is when you are changing a mainspring.
The sear screw is not supposed to be bent, if it is, it should be replaced. NO screw should ever be bent.
Tip: when reinstalling the sear spring, run the screw up just finger snug, then snap the spring tab into its' slot - don't try to fit it while it's compressed.
I never believed there were SO many STUPID people in this country. Start working now to take the Senate in 2014.