Nope, there is no such mod. The game doesn't have the mechanics for jumpgates, and we modders can't add them, because all game mechanics are hardcoded.

Still, there is a dev-post on Steam, indicating, that they might add something like this in GalCiv 3.

  The nearest to jumpgates is stacking military starbases.  So a ship near 16 starbases with ship-speed upgrades to +3 gets (16 x 3) = 48 speed bonus.

  With a max of 4 starbases per sector, you can pack 16 near one corner of 4 sectors. 

  I guess you don't like putting engines on your ships.  3 hyperwarp drives on a massive hull gives them a ship speed around 17 with enough space for weapons and defenses (assuming you've researched) to beat most ships.  They can get anywhere in the largest galaxy within a few turns.