Here is my opinion regarding Lev 19:3 regarding fearing parents.
Check out my ten commandments page. It shows the hierarchy of the commandments as I understand it.
So basically, your should fear/honor your parents ONLY if they follow Torah and worship One True God. If they dont, then you are free from the command.
Check out Deut 33:9 - the explicit answer is right there.
At the same time, I'm hesitant to make any claims regarding command priority, especially when dealing with things which would be deemed implicit commands (i.e., saving life). Also I do not think that parents' non-observance entails not honoring them. Honoring them would not necessarily require one to follow their way of life or obey them. I'm just unsure about what "fearing" would entail.
Dt 33:9 is interesting in this context, though I would hesitate to enforce that as a permission to not obey certain commands.
I do understand the concept of there being a priority of God before parents, so it would make sense that their lack of that priority would cause some potential interference whenever trying to honor or fear. I'm not sure how one is to "fear" one's parents when one might not respect the paradigm of parents (e.g., in the case of observance and non-observance).
I think there still is applicability to those two commands even in the case of them being non-observant. I'm just not sure how, especially in regard to "fear".
There is explicit reference (although parents are not explicitly mentioned) in Deut 13:6-11 as well.