Both decisions would be reasonable... from different points of view. From an emotional standpoint, saving Sakura is reasonable, since, well, it's an EMOTIONAL decision. From a purely logical standpoint, though, given how the situation was ALREADY shaping up to be lethally dangerous, the SAFEST course of action for everyone else, be they involved or not, would have been to eliminate her.
To err on the side of caution is what someone who uses cold, hard logic does. It has nothing to do with morality, but with thinking in the safest possible terms and in numbers. You may not LIKE it, but it's no less reasonable a choice than yours.
Also, your claim that what Shirou did is what the majority would do is... how can I put it delicately... a load of crock. Shirou is NOT a good example of the majority of humans. The majority of humans, in a situation like Shirou's, will primarily think of THEMSELVES, and anything else comes after. You know that very well, and if you attempt to say otherwise, then you clearly are either in denial or in desperate need to get out more, because for every one person who selflessly helps someone out of mortal danger, I can show you 50 more who will viciously elbow the person they called friend moments before in order to be the first to reach safety.
It's the nature of survival instinct, and it's the ugly side of humanity that rears its head when a situation of danger and stress comes forward.
And no, mothers saving their children doesn't count as proof in your favor, because it happens to be the one exception to the rule - instinct also tells us to prioritize the future generations, which is why, among other things, when in a situation of mortal danger any living thing's first instinct tends to be to seek out the closest female and mate, and why parents prioritize their children. Again, survival instinct.
Shirou... goes against that, and because of that he and his actions actually represent the MINORITY that is genuinely capable of self-sacrifice in spite of genetics. Most of us... aren't like that. There's a reason why the media make such a big deal of martyrs to a good cause - it's because they are NOT common.
So don't say what Shirou did is 'what the majority would do'. What the majority would do is, more likely, carry a knife in their pocket and stab Sakura in the back at even the most minor sign of danger she could pose.
Humanity didn't get this far by being selfless, unfortunately.
Finally, uh... technically, 'selfishness' is also defined as 'the act of doing something to one's advantage in disregard of others'. Choosing intentionally to save Sakura even though he was warned of severe danger to others... sort of falls in the 'doing what he wants in disregard of others' group.
Selfishness isn't necessarily a BAD thing - it is actually a quite natural part of human nature, since without it we wouldn't have lasted very long as a species - it's just that it's often tainted by other, much more negative aspects like greed and hatred. THEN it becomes bad. In and of itself, selfishness is simply placing oneself - including one's own opinion and desires, and yes, even the heart's desires, like the second time you mentioned he refused to kill Sakura, above others'.
It's not negative per se, but in Magic terms, it's associated to Black. Black CAN have positive angles, you know - you seem to be arguing this based on the perception that black = evil and thus Shirou can't be it, and while this is often the case (as Black is also the color of ambition, among other things), there's been many cases in Magic lore where Black was unquestionably the GOOD color, while White and Green turned out to be quite monstrous and Red turned out to be so self-destructive it consumed anything in its vicinity too.
Examples that come to mind include Dakkon Blackblade, who for all that he was overly concerned with his personal freedom had good reason to do so (you'd be cross at being someone's toy if you had your soul stolen by some jackass Planeswalker too), Toshiro Umezawa, who while being, well, a bandit, was also pretty much the most loyal friend you could ask for, Nissa Revane who for all that she was a bit arrogant (but that's an Elf trait, it has little to do with color lol), was also genuinely attempting to save Zendikar and was mistrustful of Sorin for good reason - he was a vampire, and Nissa's experience with vampires was less than pleasant, Sorin himself who spend centuries of his existence protecting Zendikar and the multiverse from the Eldrazi, and Teysa Karlov of House Orzhov, who was actually instrumental in saving Ravnica from the Guildpact mess.
Just saying...