If it's an issue of engineering than perhaps there could be techs increasing the angle from the pathway you can jump at. Start with 45+/- and improve it up to 90+/-? Would add a few more techs and might add another interesting tactical element. Different races might be better at it too.
you missed the point that its a gameplay issue

I prefer onwer/allies jump through field, enemies travel through field. However, I think there should be some research requirement for the onwer/allies jump through. Perhaps make it a to step research; first step gets you onwer jump through, second gets you ally jump through. Also, I'd prefer a orbital facility to enable the jump throughs and a capital ship passive upgrade that would allow a grouped fleet the jump through if the orbital facility is not present.
I was thinking perhaps this would be a vasari thing (phasegate and whatnot). however its too broken for a buildable/researchable element. it already takes a while to get through the G-wells, allowing someone to get through them very quickly will irritate the problem.
I think the vasari should be able to build phase-manipulators capable of allowing ships to jump through a gravity well in
their own territory. but this type of ability should not be open to the advent or the TEC.