In my opinion MWJ is one of the most unfun abilities in the game. The game's essential part of "hunt down the frigates" in order to fight for point control becomes very dangerous since that escort can always summon his bigger brother. In 2v2 it is even more ridiculous, since it allows you to turn it into 2v1 as you can teleport your flagship into enemy backline while your enemy has to reorinate his frontline in order to help his sandviched teammate.
And thing is, it has next to no counterplay. It is instanteneous, get out of jail free card that dodges torpedoes, all bombs including stasis bubble. It gets you out if you had bad positioning and also has insane offensive capability on top of that. Don't even get me started on how ridiculous it is with eldar flagships which are already really hard to catch.
Personally I'd remove MWJ altogether, as it is very unfluffy and warps the game balance too much (pun intended). However, since it probably will never be removed, here are my proposals to add some counterplay against it. Cherry pick them as you like.
Proposal #1: MWJ has the same animation and channel time as Warp Jump. It can be interrupted in the same manner.
Proposal #2: MWJ should only target scanning range of your ships, no hopping to teammate.
Proposal #3: MWJ leaves a noticeable mark on location of it's arrival. Enemy vessel entering that zone interrupts MWJ.
Proposal #4: MWJ is removed from all eldar factions and is replaced with anything else. Eldar are good at punishing split enemy and have insane map control even without it.
Proposal #5: MWJ has a limited range. 18k is more than enough in my opinion, no need to be able to literally cross the entire map in a few seconds.