Lots of good points, thought I might throw my 2 cents in as well.
This argument if pretty similar to the one had back in the 80's with the old GDW game Renegade Legion. The naval portion of the game system was called "Leviathan" and their jump drives worked very similarly to whats being discussed here. Their solution to prevent long distance jumping was detection, and charge build up. Their movement system was "Newtonian lite" but with more advanced rules that added much more realistic thrust rules.
1st- Deep strikes.
Overjumping sounds like a great idea, and adding in a penalty to accuracy sounds even better. To add to that, as a limiter to prevent "drive by nuclear annihilation", add a tech line to jump accuracy as a radius. So, much like jump drives work in Aurora now, add a tech multiplier that would add to the accuracy of your jump. Sort of a jump radius limit. As you exceed your "safe" jump limit, your chances to introduce errors starts to increase significantly. You could even put it in bands, so if its inside the "safe" margin, its a milk run, or maybe its the ONLY jump transition that civilian ships can use. Jumps further out, say in the 2x or 3x band, get increasingly dangerous, to the point of losing ships to systemic failure or running into objects in space.
In Leviathan, jumping ships build up a charge in T-Space "heat shimmer", that if it exceeded a months duration, caused systemic failures in the ship until something catastrophic happened. The only way to bleed off heat shimmer, was sitting around in real space letting it slowly dissipate.
Skipping the handwavium aspects of jumping, you could make the argument that jumping produces short lived high energy radioactivity on ships, that needs to disperse. So, you could say the limits would be either accuracy or the build of of radioactivity/high energy particles or both.
So there is one option.
2nd- Detection. In Leviathan, T-Doppler arrays sat in most major systems, and even in some ships. As a fleet transitioned into T-Space they had to build speed in precise alignment with their destination prior to jump transition. Once they transitioned into T-Space, they traveled in a straight line path to the destination. The longer the jump, the easier it was to detect the moving ships/fleet, and relay the detection and path of travel information off to naval forces in the targeted area (done via FTL communications using the same principal as the jump drive). The locals then got to arrange for a warm welcome. So, in the Renegade Legion universe, while you COULD deep strike, the chances were very slim to have it work in a well developed area with good detector arrays up.
So, the way to limit deep strikes and keep more of an island hopping/forward base type system in place would be to include something like those to mechanics (or both). You could also make these tech research items, so that it would be POSSIBLE to do a interstellar drive by at low rish, due to your opponent not having spend any points in that area....