....My solution is to make the rocket int level VII rather than level IX....
Great minds think alike -- that was part of the solution I finally implemented, after wasting an hour of my life that I will never get back.
Anyway, here is what I did.
1) Re-ordered interceptor models. Changed the 1950 supersonic interceptor from model 7 to model 9, changed the 1943 Komet rocket interceptor from model 8 to model 7, and changed the 1946 Natter rocket interceptor from model 9 to model 8. Moving up the rocket interceptor tech by one slot will reduce the upgrade advantage somewhat (although it still exists). This is similar to what you suggested.
2) The Komet tech will require the 1943 regular interceptor tech rather than the 1940 tech. Therefore, you will discover the Komet later in the game. To take full advantage of the cheap upgrade of of your 1940 interceptors to the 1943 model, you would have to wait a few months with your interceptors on "do not upgrade" until you have finished researching the Komet tech. The air war heats up in 1943, so the USAAF and British will be bombing the crap out of you in the meantime while the Luftwaffe has obsolete interceptors. Or else you could just pay full cost and immediately upgrade 1940 Fw-190A to 1943 Bf-109K Kurfurst after discovering the regular 1943 interceptor tech.
3) The Komet tech increases interceptor build time by 56 days (40% of the 140 day cost of the Model 0 interceptor, kind of like having a negative Aircraft Assembly Line tech). This extra 56 days partially offsets the upgrade bonus, although upgrading will still be quicker and cheaper than it should be, and Germany has an advantage.
4) I decreased the build time of the Komet and Natter by 56 days so rocket interceptors take the exact same time to build as they did in TRM v1.07
I fixed the events, icons, tech pictures, aircraft model names, etc. to correspond to these changes.
BTW, I got rid of the -3% IC hit that I had originally proposed. The solution above is much more complicated but it is more reasonable. The issue is resolved as well as it can be.