I remember, and I mean, if you don't want it to work, that's totally okay!!, but you indicated you were interested in maybe finding a way around that, so here is my rationale:
In Marina, yes, Lelouch's geass is totally subject to willpower checks. That's part of the limitations placed on it. But in Botani, there are no power restrictions, so it's at its full strength, and in Lelouch's canon, geass is not really subject to willpower checks.
Nunnally and Euphie both resisted it (though in Euphie's case, Lelouch specifically theorizes that it's because his command was so completely a betrayal of who she was as a person), and they resisted substantially, but in the end they both did what they were compelled to. Nunnally wasn't able to break the other curse placed on her for nine years, and it took Suzaku a full year to work out a way of bending (not breaking) his own curse. Lelouch commented of Suzaku that even that much was a testament to his tremendous willpower.
So, arguably, but again not if you'd rather not, a full-strength geass could work on Zero, albeit with suitable resistance. :|a
I'm also totally up for the CR that could result from a failed geass too, though. (If it failed completely, Zero probably wouldn't know Lelouch had tried to do anything to him -- Lelouch has tried to use his geass on a few people, and they've all just given him weird looks, rather than asking wtf is up with his creepy eyeballs, so I'm forced to assume his magenta geass eyes aren't really visible except to other geass-users.) (CODE GEASS IS A BIT INCONSISTENT ON THIS POINT.)