Most immediately, the reorganization drives the Syrian opposition further toward Islamist extremism – which has not been particularly beneficial to the Syrian civilians who come under these groups' rule. By joining the "Islamist Alliance," which includes Jabhat al-Nusra, rebel factions are showing that they are more willing to adopt or at least tolerate the group's extremism. As a sign of how bad things have gotten, al-Nusra is actually somewhere near the ideological center of the rebel movement; the al-Qaeda group Islamic State (ISIS), whose fighters are streaming into Syria from Iraq are considerably more ideologically extreme.
More medium-term but perhaps just as dangerous, this deepens fissures among the Syrian opposition. The odds are rising that rebels will turn against one another more fully, as they've already done in some isolated incidents. That's not just bad because it weakens the rebels and exacerbates stalemate; it could risk a second civil war, whether after Syrian leader Bashar al-Assad's fall, should that happen, or in parallel to the current fighting.
There's another big implication here, particularly significant for the West: the window when Western countries might have championed a rebel faction could have just closed, possibly for good. "The scope for Western influence over the Syrian opposition has now been diminished considerably," Charles Lister of IHS Jane's told Sly and DeYoung. The United States would now have a harder time than ever finding a viable and ideologically palatable Syrian rebel group to support.
For a time, rebel groups seemed to be holding out hope for Western support. But fighting has been raging now for two-plus years. Direct military support from the West has been tepid; American small arms started appearing on the battlefield several months after President Obama first publicly pledged as much. In the meantime, Assad's forces have been gaining ground. And Syrian rebel groups increasingly have to worry about fighting with ISIS militants.
One line you often read, in stories articulating the United States's many unattractive options in Syria, is that there may or may not have been a window for a Libya-style intervention early on in the conflict, but that we'll never really know. We may now be at a similar point with the window for championing a branch of the opposition.
It's not hard to understand why, if only for tactical reasons, some rebel factions might want to jump ship from the Western-aligned umbrella group that has not served them particularly well. That this also has the effect of shifting the Syrian opposition more toward ideological extremism, and away from potential direct Western backing, is another dispiriting turn for a civil war that has had many.