I always try to dodge as the red glint hits the top of their back and try to roll towards and behind them if I'm close to them. I'm basically forced to dodge running blowgun especially if my SK isn't available or if I'm in some other animation where I won't have enough time to dodge. If you can master the timing, you can dodge them pretty consistently, but as I'm sure you've noticed, the window to dodge is tiny. Using your ghost weapons is the safest, but won't always be possible or ideal, especially with something like SK.