I agree, where the parents stray from the will of the Lord, the call for obedience is gone. The verse better translated "Children, obey your parents as if to the Lord". Not freed for total disobedience; never obeying, just freed from anything that is against God. Is it a minor point here? Maybe - but I thought one worth making.
As for honoring - my studies have brought me to a slightly different place which I offer as another view - I am to honor my parents. Period. This verse does not carry the 'in the Lord' qualification, it is a new statement. But what is honor? Lack of disrespect.... I've been able (at least some) to fulfill this with politeness on the phone when required, no more screaming at them for their "crimes against me", etc etc. They know what they are - the Lord will deal with them. (Romans 12:19 "It is mine to avenge, I will repay.")
And if there's any doubt where to draw the line, there's Col 3:23 "And in all you do - do it as to the Lord".
Just my take.
ps - regarding the wife/husband who is married to an unbelieving spouse. Let's not forget 1 Cor 7:16 "How do you know, wife, whether you will save your husband? Or, how do you know, husband, whether you will save your wife?" Yes, he's talking staying married here - but how do you fulfill that without honor?