Jesus is present before us at Mass, under the appearance of bread and wine. He doesn't look like a physical human being. We accept His true presence as a part of our faith. Signalling that faith by kneeling in front of the worldy "absurdity" of Jesus' presence under the appearance of bread and wine is an excellent reminder, and can't possibly bewrong . Especially when it is the norm, and flouting the norm can indeed be a way of expressing rebellion of the heart, no? A "good hearted" person, physical impossibilties or frailties aside, should want to (at least) kneel before his God at the times He is both present and visible.
In the old days, many Eoropean churches were built without pews, and only the elderly and disabled would sit on chairs or benches along the walls. That was largely a practical matter. In those days of real, widespread faith, churches were packed to the point where the entire nave was SRO, and both sitting and kneeling were impossible, or at least awkward. This is hardly the case today in nearly every venue outside of a papal Mass or the concluding Mass to some major pilgrimage. The letter of the law might call for more restricted kneeling in favor of the existing architecture, but, in the places I've been in Italy anyway, people seem to have no big problem kneeling on the (uncrowded) floor if nothing else is available. Charis with kneelers folding down from the chair ahead seem to be pretty common.
It says a lot about this pastor and his congregation when they create such a stir by bucking the bishop's clear and rubrically correct directive. God, as you note, looks at the heart. What kind of heart is betokened by pastors and congregations who will not obey a clear and correct directive from their bishop, in matters where he has both competence and undisputed authority? What kind of beliefs do these people hold about the Eucharist?
In the end, they should kneel, not to impress their neighbors, or even themselves, but because it is a "right and fitting" posture, as the West understands these things, to kneel before God. They should have the humility to do so, and the wisdom to see that posture as an honor that none other among God's creatures has the station or sense to adopt.
No problem with that.