Is this sentence parallel even though the noun "being honest" is a gerund and the noun "deception" is not?
"Living a life of being honest to yourself is better than living a life of deception.
Yes, it's parallel. No problems here, except that being honest with yourself is the usual way of putting it.
"Living a life of being honest to yourself is better than living a life of deception."
"Being honest" is not a constituent in your example (so it can't be a gerund). However "being honest to yourself" is a constituent -- it is the NP (noun phrase) object of the preposition "of", and it is being contrasted with the NP "deception", which is object of the second "of". The latter NP contains the noun "deception" (though that NP could contain more than just that noun, such as a modifying adjective, for example).
You could call "being" a gerund, I suppose, but I wouldn't, because some take a gerund to be a kind of noun, and as tchrist noted in a comment, "being" is a verb in this construction.