I prefer Hill-e-an. Just because it's the root of Hyrule doesn't mean it has to have the same vowel sound.
There's a dinosaur that used to live around here, Edmonton, called Edmontosaurus, and it's Ed-MON-TO-saur-us, not Ed-MUN-TUH-saurus as in Ed-MUN-TUHN. Similarly, we live in the province of Alberta, Al-bert-AH, but we're Albertans, Al-bert-UHNS, not Al-bert-AHNS.
Like mentioned earlier, it could be "hill" like in Transylvania. Tran-sill-vain-e-a. It's not Tran-sighl-vain-e-a.
Personal preference, I guess. I don't think "Highlia" sounds dumb, I'm just not used to it.