When our submersible pump died in Spring 2003, (high desert So Cal, clear but mineral laden well), they pulled the pump and it's galvanized piping.
Tons of rust fell off - the pipes had to be shot thru with rust. Maybe leaking had cause the pump to fail, for all I know.
Anyhow, there had to be a half a wheelbarrow full of rust residue piled on the ground, right where they un-threaded the old, nasty galv pipes - 220 feet.
They replaced 'em with Sch 80 PVC (1 1/4" I assume) and that would ensure no more rust in the well.
It made a huge difference over time. Before, we had a red tinge in the water, rust particles in our sediment filter.
It probably got a bit worse at first - they pointed out a certain amount of rust fell down in the hole, but we noted slowly over 6 months, the last traces of rust disappeared. (I belive they used bleach to re-sanitize the well upon completion)
I think it's normal for your well water quality to be upset when unsealing things for repair, at least for a while.
Hard to say which is better - we keep using ours as normal. We did buy RO drinking water before & after, so to us it mattered not.
If you only wash, bathe & shower - no drinking, what could be the harm in contining to use it as normal ?
It will probably clear up faster if you pump it out, right ?
Hope this helps....