It's not that he's trouble for light siders. Every light sider I've ever had has trounced him but good. But then, every light-sider I've ever made was a guardian. Malak's defense isn't high enough to overcome the ridiculous bonuses a guardian gets to his hit rolls, but his saves are enough to put force dependent people in the hurt.

You are remembering to force breach him before trying to stun, right? I seem to remember Malak using force resistance abilities. If that's accurate, you'd need a miracle to get off a spell without breaching him first.

What's your equipment like, and which version are you playing? Did you remember to snag yourself the star forge robes while you were going through? If you're playing PC, did you get the circlet of saresh on Kashyyk way back when? Anything at all that can boost your wis and chr helps, since Malak does have such high saves.