This is really old, but whatever.
According to Aoko, Shiki can see the "end" of everything. She compared his ability with seeing the future.
According to Rin in FSN, Heroic Spirits are removed from time- even if they die in the real world, they are not killed.
I believe Shiki would be able to "kill" the connection of a Master and his Servant, or even "kill" the servant. Still, I believe that killing the Heroic Spirit is above his abilities. Ryuogi can proabably do it since she can kill concepts, but whatever.
Shiki definitly can't fight against a servant in equal ground to begin with- see some Nasu commets about Melty Blood:
"At this point, "MELTY BLOOD" caused a major contradiction.
Since this was a fighting game, the position of the protagonist, Tohno Shiki, a character that could participate in combat only by means of trump cards, was reversed, and he became involved in the story as a protagonist that can "fight normally".
"....Right. The characteristics of the characters in "MELTY BLOOD" had either been exaggerated or restrained from what they had been in Tsukihime."
"Using cards as an example, Shiki of Tsukihime would be a 3 of Hearts. But the Shiki of "MELTY BLOOD" would be able to fight normally as a Jack of Spades."
So, if he can't even fight against MB characters, how would he be able to fight against a servant to begin with?