No one will be offended, I promise. I've been to plenty of weddings like that and people generally understand the constraints of space.

I wouldn't go to great lengths to apologise or explain to guests why they're only invited to the reception and not the ceremony. Just something short, sweet, and cute. To those only getting an invitation to the reception, I would suggest using wording that would make them feel like it is the most special reception and they would be the most cherished and special guests to you for coming. Flattery always works best if you ask me