I'm afraid it's not safe. As you surely will know (though many "normal" passengers won't), soft train fittings such as seat cushions will protect passengers if the train flips over in an accident, or if there is an emergency/sudden stop... etc. Put another way, without these fittings, the vehicle is unsafe because of what happens when an unrestrained passenger comes across a sharp metal surface in an accident. The fewer dangerous surfaces there are, the better. Not all hard or sharp surfaces can be got rid of - luggage racks and some light fittings do spring to mind - but minimising them is important.
I would at the very least have expected that row of seats and the row behind to be cordoned off until it can reach a location where a seat cushion or even unit swap can be undertaken - or the train can be taken out of service. Passenger safety comes first. You can't have the situation where passengers are allowed to travel on an unsafe unit (or part of a unit) simply because it's more convenient. Overcrowding is dangerous, too, but it can be managed quite a lot more effectively!
As far as I recall, more modern units such as (to take one example) 171s have strong plastic fittings which prevent the seat cushions from coming off by being tugged at, but are flexible enough to withstand vandalism. It is certainly quite fiddly to remove a seat cushion from a 171 if you don't know what you're doing!