Japhy, you have such a beautiful obedient soul, and I appreciate your sensitivity. Can you ask yourself if God was offended by folks standing around the altar, rather than remain in the pew? Do you really think He was?
…His motive may be pure, even though his action was not in accord with the rubrics…
While you seem to have fronted this question as if there were an obvious answer (and I happen to agree that there is), you don’t seem to have bothered to seriously ask what that answer is.
The same Christ who told us “If you love me, you will keep my commandments” is the Christ who instituted the Apostles with authority and told us them that “He who hears you hears me.” The Church, Christ’s spotless bride, commands us in His place. We are bound to obey Her because Christ Himself told us He wants us to listen to Her as if we were listening to Him. So if someone is intentionally disobeying Christ in His Bride, you can bet your boots He will be offended by that individual’s refusal to love Him.
“We obey God, and not men.” So if a priest acts outside of His capacity to teach us with God’s authority, we are bound
by love of God to disobey the man and follow God (in the voice of His Church) instead.
Lastly, a good intention can never rectify a fundamentally bad act. If it is never right to disobey just ecclesiastical laws (outside of cases of necessity, which knows no law), then being really nice or “caring” while we exhibit a lack of love is not going to make that act any more justifiable.
The general rule of liturgical praxis is “Don’t draw attention to yourself.”
This, of course, must be held in tension with the fact that we are bound by liturgical law
under pain of sin. That means there is a limit to our quest to be inconspicuous. The idea of not drawing attention to oneself is so that one does not take attention from where it really belongs - on the sacred action of the Mass. If you have
a range of licit options, it is often good to suppress personal preference and blend in with the rest of the assembly.
But, on the flip side, if being obedient as inconspicuously as possible still draws attention to you, then I would argue not only that you have no other option but that, in fact, it is good for everyone to see your ‘deviant’ practice because it will get them wondering why you did what you did. Hopefully they’ll find out it was because they, as well, are bound to do at least that.