I agree that holding hands at the Our Father should be reserved for families and those with whom we feel a similar connection. This seems to be the approach approved by Rome. I also think this would be an easy thing to fix if the bishops and pastors wanted to be serious about it. Does the practice cry out to God as an affront, an abomination? I doubt it.
Have we considered why it is so popular? Yes, it has a feel good aspect. But I think there are other reasons. After the faithful run the gauntlet of which Penitential Rite, which Responsorial Psalm (or the substitution allowed but not printed in the missalette), Credo or no Credo, which Eucharistic Prayer, and which Mystery of Faith to give their “active participation” to, they can actually stand and know exactly, every Sunday, what to say and do. And the (over)empasis on community makes handholding seem right. I may be reaching, but I think is almost a psychological release for the congregation to behave this way. However misguided, it does make sense that it has become the custom…no need to be unsure of what to say and a way to be a participating community as they have been taught.
In short, it comes partly from the structure of the Novus Ordo itself.