I had a look at the Prophecy map, and from Alcor, you can hop to Vega, then Proxima, Sirius, and Sol. That's very few jumps between Sol and Kilrah. Makes me wonder how Confed managed to keep that main route secure, while patrolling other areas such as Gemini and Enigma sectors at the same time.
My theory - and note that that's all it is - is that during most of the war Vega sector was reasonably secure. That was where the main thrust of the first Kilrathi assaults was aimed at, and it stands to reason that this was the area with the largest concentration of Confed vessels as well. Certainly, the first thing Blair did was help drive the Kilrathi out of the sector
.
The Enigma and Deneb sectors were of course way of outflanking the Confederation - especially Enigma, where the Enigma System (in which the Kilrathi had established at least a foothold) offered
two jump routes that could get them to Sol in just four jumps. Obviously, however, the Enigma offensive faltered and died after the disaster of '67, when K'tithrak Mang was lost and the K'arakh, Shariha and N'tanya colonies defected. From this point on, Confed seemed to be on the offensive in this sector, and probably remained so for the rest of the war. The Kilrathi did try to regain the initiative with their surprise offensive in Deneb, where they reached the Confed Sector HQ in just six hours after launching the attack. This gave them access to several jump routes leading into "northern" Enigma (Grills quadrant) and "southern" Vega (Day quadrant). The Confederation obviously managed to re-take the Goddard system soon afterwards, but probably not much else. Either way, I don't think the Kilrathi were ever driven out of Deneb altogether - the Concordia went down fighting off an attack which must have come from the Deneb sector, because the only other route into Vespus led through the "southern" Enigma sector (Isaac quadrant), where we've already seen the Kilrathi soundly beaten
. However, later in '69 the Confederation was able to re-take the jump route into Vespus (in other words, the Cardell and Morpheus systems, mentioned in the WC3 intro). That, however, is as far as they got, and Blair spent the first half of WC3 defending Orsini (in Deneb - it is possible that this system was also just re-taken, but it may be that it had never been lost in the first place) and the Day quadrant of Vega sector.
Mind you, by this time the war (especially after a certain battle in Sol System
) was definitely going to hell, and the main jump route in Vega wasn't really secure any more - the Kilrathi had firmly established themselves as far as Alcor, and were probably trying to capture Vega system (if they hadn't done so already). But at this point, our hero dropped the bomb on Kilrah and we lived happily ever after.
So, I guess that answers your question about how the main jump line was kept secure - with great difficulty
.
Oh yeah, we shouldn't forget to mention Gemini. Not that there's much to say. Both sides treated it as a backwater - and if you look at the distance between Kilrah and the S'kh'haral quadrant in Trk'pahn, it's not difficult to see why. For the Kilrathi, launching an offensive here would have been a logistical nightmare. So, they mostly just sent raiders into the sector. These raiders caused a great deal of trouble - especially during the Retro insurgence - but fortunately a certain Privateer (
) helped keep them at bay by killing the commander of the local Kilrathi forces.