Have you tried the "flip" stop technique? It prevents a lot of that.
I've never tried the "Flip Stop" technique. Interesting. Looks like it works pretty well.
What I have always done is this:
1. Shut off the valve at the pump/bottle.
2. Disconnect the stove.
3. Open the stove valve (the one on the stove, NOT the bottle).
4. (Make sure stove is cool first) Hold the stove in my hand with the supply line down, and swing my arm, so centrifugal force drives all the liquid fuel out of the line. This leaves the stove with no fuel left in the line.
5. Release the pressure from the fuel tank by unscrewing the pump just enough. Some fuel sprays out, so I do get it on my hands. Using Coleman fuel, it evaporates quickly and doesn't leave an odor.
So my method is certainly messier than the flip stop. I'll try flipping it next time I use the stove.
As for flare-ups: This is the biggest problem with liquid fuel MSR stoves. It is hard to tell people how to do it, but I have never had any trouble. Simple instructions:
Open. Close. Light. Wait until flame almost goes out. Then open the second time.