Because the STV trolls were run out of their home by them, and the horde 'took them in'. That's why, in a nutshell.

Not quite correct - the Darkspears got chucked out of Stranglethorn Vale by the other Gurubashi tribes for being too violent and uncivilized. They settled on some islands near the Maelstrom, where they met Thrall, who was busy fleeing from Lordaeron. After helping the Orcs defeat some Kul Tiras sailors, Thrall, Sen'jin, and the lads were kidnapped by the local murlocs, who planned to sacrifice them all to their deity, a "sea witch".

Naturally, this didn't go according to plan; Thrall broke out, rescued his peeps, and killed the murloc high priest - a little too late to save Sen'jin. The sea witch was pissed that they'd killed all her worshippers, and proceeded to sink the island under the sea. The Orcs and Trolls high-tailed it to Kalimdor, where Thrall granted the Trolls the Echo Isles. They lived happily there until Zalazane kicked them out.

So you mean to tell me that if not for Murlocs, trolls might have gone Alliance?

As someone whose first love in WoW was playing a Troll but wound up playing Alliance due to having a lot of friends on that side, I've got to say.. I really hate Murlocs even more now!

What makes you say that they might have joined the alliance? The rest of the gurubashi trolls are no friends to Stormwind.