The reputation system in ME3 is a bit weird. I think it's more than just having all paragon or renegade, but there's also an overall score that you can't really see in-game. Maybe your total rep wasn't enough? Mind you, if you've imported from ME2 then you should have had a good head start.
I don't think I've ever had a greyed out option with an imported character. Hell with that particular instance, I had both options available and that Shep hardly has any paragon on the bar. So yeah, it was probably a glitch.
Incidentally, I'd also reprogrammed the heretics with that Shepard.