Well, there's always the "Leave it alone" choice: Cloak a Raid Starship and get close enough to shoot the Warp Gate, and then just ignore the whole mess.
If you don't like that, you can try the long-slow grind, using Neinzul Enclave Starships to flood the system with long-ranged chip damage.
If you don't like that, or it doesn't work, you can fall back onto getting a cloaked Warhead close enough. One or two warheads should be enough to kill almost everything, leaving you with more reasonable remnants to clean up with Bombers, etc.
Finally, if you absolutely MUST, you can always Nuke it. That will "solve" the problem, for certain definitions of the word.