The jumpgates are of strategic and military value for both sides, because they allow them to conceal their fleet's movement. As teammembers explained before, subspace sensors can only detect that a gate was activated. They can't detect how many ships, what kind of ships or even if any ships at all were sent through, were a jump powered by the ships drives gives the people behind the sensors a good idea of what caused the flare on their instruments.
Then there is also the matter of jumpdrive charging. If you came in through a gate, your drive is fully charged to make a jump out of there if things get too sticky. If you use up the charge for jumping in, then for better or worse you're stuck there till your drives recharge.
As for the situation in the mission: They did make the gate pretty impassable. They put a destroyer and Serkr in front of it. Under normal circumstance that wouldn't have been just sufficient, but actually overkill for the foces they expected. What they didn't know was, that the UEF is able to jam their beams and thus the hunter became prey and had to run or be destroyed.
Also Laporte was only able to call in support from the Toutatis, because she was using a GTVA transponder and thus wasn't affected by the jamming.
That is why I like this mission a lot. It shows that the GTVA and Steele are just Humans too. They can make mistakes and can be caught by surprise.