Trying to figure out a way that a ship in Hyperspace can have a part removed/disabled that wont prevent it from dropping out of hyperspace, but might keep it IN hyperspace.

In one old WEG adventure (The Isis coordiantes) the ship they were on was sabotaged and there was a 5 in 6 chance that if they "Dead dropped" out of hyperspace they would be turned into a fine dust.

Best i can come up with is a missing hyperdrive inhibitor that isn't bad in itself, but could be bad if they somehow go off course or a uncharted mass gets in their path

Have both the bridge and engineering damaged before the jump happens.

Your players need to find a way to reach either and/or another means to cause the hyperdrive to be either ejected before it blows up the ship when it tries to shut down or they eject inside their version of Star Wars Rebels Phantom?

See Season 1 of that series to see what I mean by that!

I really don't want "damage" just some sabotage a curious Kowakian monkey lizard that is a kleptomaniac might cause

This is what technobabble handwaving is all about.

"You are in hyperspace approaching your destination. The nav computer beeps, indicating that the hyperdrive is not responding to the signal to re-emerge into realspace." PC's check and a quick diagnostics finds that the Hyperdrive interface coupling (insert your own cool technobabble name) is missing. Someone must be onboard and stole it! Now start the search on the ship with 12? rounds to find the Kowakian monkey lizard, recover the coupling and re-install it before you hit something in hyperspace. Also, when you re-emerge into realspace, you are not at your destination, but happened to emerge near an Imperial Weapons Test (Or Hutt Spice transfer ... or whatever other problem you want to hand them.).