If ships were destroyed it would have severe gameplay implications to the Vasari player, it wouldn't work and it's rediculously harsh considering we could be talking about wiping out an entire fleet for 1 structure loss.

Forced back to the well?  It seems just as feasable that the gate is closing behind the fleet at the same rate as the fleet is jumping I think.  Plus you just made it impossible for the Vasari player to send his fleet straight back to reinforce not to mention the cost of the phase gate and the fact he can't use it to bring in reinforcements through Returning Armada.

I think it works fine as it is.

Vasari players don't really have the option to NOT use the phase gates ,with the current Interface. If you tell ships to go to planet X, they use a gate if its faster.

So if destroying the gate sent the ships back, the player would need to manually guide those ships from planet to planet in a transport route that ignored the gates, because having them sent back would make getting reinforcements there take even longer. It'd make the gates more of a liability then a help.

I see why the idea makes sense logically, but sometimes gameplay can't follow logic.

Oh, even more fun...how about they drop out of phase where they are?  That could be real ugly.  It would make some sense logically speaking, but gameplay wise it would hurt. 

Ahhh!  So in this case, no big deal.  They have already jumped.  Jumping is a function of thier jump drives and not of the gates then.  That begs the question, what keeps any ship from learning the coordinates of a point in space and jumping directly to it, bypassing the jump lanes?  Maybe the gates setup some kind of buffer for the jumping ships that allows them to jump?  A temporary jump lane?  Then the energy produced by the ships in transit keep the gateway open long enough for them to complete the jump. 

Yeah, think of a phase gate as a giant hyperspace cannon. It sends the ships in the right direction with the right power. 

Why can't any ship find the co-ordinants? Well they aren't just the XYZ you're used to, there is also time to take into consideration. Since the gaps in space are so large, you have to have a mini wormhole to give acurate data. If A ship sends out it's sensors, discovers where it is they want to go, by the time they've received the data, the co-ordinants have changed.

With a phase gate, they are entering phase space, (like a mini wormhole) so they can receive the data almost real time.

Perhaps the two gates sync togather and calculate a route.  This infomration is giving to the nav computer aboard the ships.  The vasari then sync to the gates and follow this route.  It would not matter after they get into phase space since the route is already calculated, and the correct sync is already down.  Think of them like a gun.  You pull the trigger and the bullit comes out.  Once you pull the trigger and the bullet comes out you no longer need to the gun.

Rofl, obviously you don't know how big of a problem 'slightly off their original jump plan' can be.

Lol.

It's just a game, you should really just relax.