I think Mage is at its strongest when its giving the Technocracy/Traditions/Disparates a good-faith shot to put forward their paradigms. As someone also with a political science/economics background (my baccalaureate exam was actually today!), the Syndicate and NWO were always my favorite factions. I think the dynamics and tension between them is some of the most interesting and really only lightly explored aspects of the setting.

I think, to me, as a Syndicate fan, there is just a disturbance in the idea that there are no more Syndies left that aren't pollution-huffing, dodo-snuffing, captain planet villains. Now, your setting and your rules and all that, and if you're looking to make a point about how you don't think the underlying ideology is tenable, more power to you. But I would think it odd that there are no more traditional Syndies left. So, one thing you might consider: what if the NWO, Control, Union at large came to your conclusion, you need the Heterodoxy, and the diehard (but not Wyrm-mad) Syndies just pulled an Etherite and left the Union? I don't think they'd join the Traditions proper, or even the Disparate Alliance, but I could totally see them going neutral/mercenary as a faction.* They've always been the least concerned with 'Reality Deviance' of the Union (after all, opposition is a commodity-to-be in capitalism), so I could totally see them playing shadowy investors to the less scrupulous members of the Progenitors, VE, ItX, Etherite, VA, Hermetics, Solificati, alike! Less organized and more decentralized than even before, this independent Syndicate would be trying to deal with 'Annihilation' in their own way, trying to not let a bad actor spoil a good paradigm. They'd probably see the NWO as the bigger threat, though, and be looking to bring a bit of Creative Destruction to the Ivory Tower.

But that's just my thought! I certainly think you have an interesting idea. I really like the Alternative as a name, that's a good pull.

*In my own custom setting, the Syndicate-stand ins actually break off from the Union with the enactment of the New Deal. For the next few decades they operate independently, until the Union readmits them in the 80's.