I think the point's been picked up on already which I would see as my main issue: glassing offers little benefit to the Covenant. As you don't have a religious unity factor to worry about, glassing is essentially what planetary invasions are. The difference is the Covenant didn't (to my immediate knowledge) bother colonising once they'd glassed, whereas the principle of sins to turn the planets to your side. Basically if you glass every planet in a row you end up being overextended (think of the issues with blitzkrieg). The point about making Covenant similar to VL is an idea I have a lot of support for, culture issue aside, maybe glassing could be a stripped to the core replacement offering some bonuses, though I suspect the potential benefits are extremely limited. For instance, though it would be nice if glassing gave a research buff (simulating artefact pillaging) I just don't think it's possible.
Tactically though, there may be an advantage to glassing. All things considered, it may be advantageous to make a hostile world uncolonizable rather than taking it yourself, for the very possibliltiy of becoming overextended. Since the Covenant have virtually no effective defense in the least, it's tough to keep the worlds you've taken - you might get caught up in a war of attrition and stall out your attack, meaning the UNSC can build up its tech advantage. Preventing colonization means the UNSC can't turtle the planet - since the defense is the main UNSC advantage in battle, it may be advantageous to glass the planets as you go and force the UNSC back.