I too occasionally check the mags in flight.
The only way I can see that you're going to have any arcing in the mag (in normal operations) is if the capacitor is u/s...then it's going to arc whether you're in flight or not, and not just when you're checking the mags! I have experienced a mag failure in this way - capacitor u/s, leading to arcing, leading to a dead mag. It is hard to find - since the mag appears to run fine...until it doesn't!
Mind you, for the same reasons Bob mentioned to ensure you're well ROP, I would recommend lower power settings when checking the mags in flight. Running on one mag will reduce the detonation margin.
Cheers,
Damon
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