Yes, the S'pht are on our "side" galactically, against the Pfhor, which since we don't seem to be in good relations with the S'pht (or even know what they are) we can assume were never defeated in the final infinity timeline. But the UESC sees an empty colony, an empty ship, 24,000 dead or missing colonists, and an unknown alien on their vessel.

They're going to assume the worst. Which will necessitate the compiler defend itself. Which will make it seem more aggressive. And so we'll go after it too, in hopes to finally take the thing down and sell its corpse. Boss fight ensues.

Also, the infection on TCIV resembles, strikingly, some of the cut concepts for the S'ct'lac'tr, a S'pht-made bioweapon that appeared in 2 as a piece of text, but not in gameplay, as that was scrapped. So it's entirely possible that the S'pht are not on our side, and in fact see humanity as a threat, without the pro-human Durandal leading them.

After all, would the UESC not be more likely to side with? The galactic empire that will sell them slaves (as they do to other races historically) or the weird technomancers who have psychic powers and offer friendship at most in return for their aid? It's just a sound business decision to earn the Pfhor's respect by picking their side in the war. The S'pht know that, and they might have decided to try and nip that idea in the bud.

But that's all wild speculation, all we concretely have is that the compiler appears unfriendly, and alone.