If you have that in writing (print out the email), then I`d just risk it. If it was a phone agent, follow-up on this with an email (or, if you're on FB, try posting your question on the Cyprus Airways page)
Alas, I fear that the agent may have given you incorrect information, as Cyprus Airways does allow two animals per crate when they're transported in the cargo hold, but only one when transported in the cabin.
Cyprus Airways has their own staff at Larnaca, and the people I know engaging in rescue work in Cyprus speak well of them.