Why not make a sort of pinpoint mission set or ark, so have it as special hk-47 missions you can do at anytime (Since Sith assault seemed like a weird reason for hk-47 to start it [Statement: Hmm, the exile is leaving to defend Telos on a possibly suicidal mission, I'll just leave on my own suicide mission making it even harder for the both of us!]).
Like have a special dialog after you've fought however many hk-50's to pinpoint the Telos location that makes it so hk-47 starts a special mission to buy his own ship with a pilot droid(which could be a playable character until you get to the Hk-base in which it would be destroyed somehow making it slightly easier for a while) or something (just a shuttle, since it also doesn't make sense that the Ebon Hawk, from Dantoine dropped off Hk-47, then went off to the ice jedi place/atris' stronghold since they knew handmaiden was in mortal danger, it also doesn't make sense that Hk-47 snook off and walked or something.), upgrade it to a point the hk-50 units wouldn't be able to detect it, assassination missions (not for the Telos one just for fun) and then have hk-47 start upgrading missions on himself and/or maybe missions to acquire his old assassination protocols he had lost (a possible way making him a better playable character for the hk base), building up to the hk base mission, give hk-47 preparation time for it. I hope all of that made sense. in summary:
1) Mission to obtain a shuttle and a pilot droid or something(maybe with Hk signitures to make it so it can enter the base? Maybe have the Hk-50 he interrogated be reprogrammed to do Hk-47's bidding)
2)Upgrading missions for Hk-47
3)Assassination missions for fun
4)the mission to the Hk base, possibly with a sort of patsy (the pilot).
5)the hk base