There are several related topics here. I'll address each one separately.
"I want to understand!"
let me know Your ways that I may know You - Exodus 33:13
First, I want to emphasize that it is good to seek understanding. It is also good to help others understand His ways. Seeking to know the reason behind a command is not sin.
Philip ran up and heard [the Ethiopian] reading Isaiah the prophet, and said, “Do you understand what you are reading?” And he said, “Well, how could I, unless someone guides me?” And he invited Philip to come up and sit with him... Then Philip opened his mouth, and beginning from this Scripture he preached Jesus to him. - Acts 8:30-35
Knowledge of scripture will only take you so far; at some point you need to understand what you are reading - and often times you need someone to be there to help you understand. If Philip had not explained the Scriptures to the Ethiopian, he would not have understood and would not have been converted. We should be careful how we respond to a person who is seeking to understand God's ways.
Your hunch is correct - all sin in Scripture does indeed have some degree of justification, although it may not be specific or explicit. I tell my kids not to eat batteries... because if they do they will die. Similarly, God tells us not to sin... because if we do we will die.
God is love. Believe it or not, all of His commandments were given to teach us love - and to show us our inherent inability to love - so we would return to God through Christ! His commandments are an elaborate attempt at urging us to return to Him! The law was given to teach us about God's very nature - that which is good and right.
Sin is a rejection of what is good and right; a rejection of God's law; a rejection of His ways; a rejection of Him. Sin separates us from God. If we choose sin, we choose separation from God - He cannot "embrace separation", "accept rejection", "fellowship with those who flee Him"... If we die in this state, we experience eternal separation from Him, also referred to as "torment" and "death".
The general justification of every command is the same. It is good to follow God. It is bad to reject God. Sin creates a separation between you and God. This is really bad for you, so you should forsake sin and return to Him.
No Explicit Justification
There are examples of commands in the Bible which have no explicit justification. Here's one random example:
They shall construct an ark of acacia wood two and a half cubits long, and one and a half cubits wide, and one and a half cubits high. You shall overlay it with pure gold, inside and out you shall overlay it, and you shall make a gold molding around it. - Exodus 25:10-11
Why those specific dimensions? Why acacia wood? I don't know. I am sure there was a good reason - and perhaps there is a Bible scholar out there who can explain it using Scripture. But to my knowledge no explicit justification is given in Scripture.
Does God Explain Himself?
Your question here was, "If there is a command without scriptural justification, what is the right course of action in defending the command?" First - be cautious about entering into the activity of teaching others about the Word of God.
Let not many of you become teachers, my brethren, knowing that as such we will incur a stricter judgment. - James 3:1
If you are called to teach, make sure you know what you're talking about before you begin making confident assertions about things...
For some men, straying from these things, have turned aside to fruitless discussion, wanting to be teachers of the Law, even though they do not understand either what they are saying or the matters about which they make confident assertions. - 1 Timothy 1:6-8
If God has gifted you to teach, and given you understanding about the topic you are discussing, the proper method of teaching is summed up pretty well here:
The Lord’s bond-servant must not be quarrelsome, but be kind to all, able to teach, patient when wronged, with gentleness correcting those who are in opposition, if perhaps God may grant them repentance leading to the knowledge of the truth, and they may come to their senses and escape from the snare of the devil, having been held captive by him to do his will. - 2 Timothy 2:24-26
The teacher must also be led by the Spirit and should function within the context of the other members of the body of Christ.
This is the most formulaic approach I can concisely offer for how to properly defend a command from scripture. I hope that helps!