??? I don't think you finished that last paragraph, there...
Anyway, if Kiritsugu was successfully killed (by EMIYA or anyone else) during the Fourth Grail War, Saber would never have Excalibur'd the Grail, and thus (IIRC) no massive fire killing Shirou's real parents, among others.
...then again, the resulting causality paradox would kinda make the absence of the fire something like losing a Zippo amidst a nuclear bombing. I think.
One major issue: Rin summoned EMIYA because her amulet (and possibly she herself) acted as a link to him. In Tokiomi's case, the catalyst he used was the fossilized remains of the first skin shed by the world's first snake, and the amulet probably wouldn't enter into it. And considering that Shirou never met Tokiomi, that wouldn't be a link.
On the opposite side, I see much potential (assuming the world doesn't go pfft!). If Shirou wasn't raised by Kiritsugu (who was extremely reluctant to teach Shirou anything at all about magic), I'd bet Kotomine would take him in. In this case, that would put Shirou and Rin in close proximity.
Without Kiritsugu's influence on his upbringing (indeed, replacing him with Kotomine), he'd probably be quite a bit more cynical and superior. Rin's high potential would rankle, leading to a heated rivalry.
...might be grounds for a mutual tsun-dere romance between them. ^_^