Vulcans can certainly have blue eyes...

Some may also have green eyes, but the only example I can think of is Saavik, when she was portrayed by Kirstie Alley in Star Trek II: The Wrath of Khan.

Saavik had brown eyes when she was portrayed by Robin Curtis in Star Trek III: The Search for Spock and Star Trek IV: The Voyage Home, and was stated to be "half Vulcan and half Romulan" in one of the scripts for Star Trek II: The Wrath of Khan (though this was never mentioned within canon), so this example seems a bit iffy on more than one count.

We've seen quite a few Vulcans with blue eyes though, including at least one from Star Trek: The Original Series (if that's what you meant by "original"). The examples below are listed in order of appearance.

Stonn (TOS: "Amok Time")

Satelk (TNG: "The First Duty")

T'Pan (TNG: "Suspicions")

T'Lara (DS9: "Rules of Engagement")

Sitak (DS9: "Favor the Bold")

Solok (DS9: "Take Me Out to the Holosuite")

V'Lar (ENT: "Fallen Hero")

V'Las (ENT: "The Forge", "Awakening", "Kir'Shara")

Regarding the question about stigma, there are obviously various behaviors which would be stigmatised within Vulcan society, subject to specific eras (mind melds were stigmatised during the 22nd century, but not in the 23rd and 24th centuries). I don't recall hearing of any physical characteristics possessed by any Vulcans which would be stigmatised in that way though.