There's a lot of ifs and buts in the situation because - as far as I am aware - the HIE dangled a fair financial carrot in front of a merged ICT, and I am not sure that they would have done that in front of either Caley or Thistle as individual clubs.
I think Caley would have been the Invernesian team to progress into the SFL - they had the far better set-up of the three Inverness clubs at the time, and could easily have achieved much the same as the merged ICT did.
As for Thistle, I think they would have done ok in the Highland League as they had a decent set-up, certainly regularly mid-table - but then again, Clach do struggle (other than their one title win) despite being the only semi-pro side in Inverness - so maybe not?