Now that CQL allows for user side timestamp (which it should, no question asked), that row deletion problem covers CQL too (actually no yet, because of
CASSANDRA-2912, but that's just a bug).
Is it possible (when Deleting, inside a thrift Mutation) to loop through all the columns that need to be deleted
That doesn't really help. The problem is with full row deletion. If you have a row with "regular" columns and with one declared counter column 'c1', then if you get a row deletion, you can insert a deletion with server side generated timestamp for 'c1', but what for the rest of the row ? If you insert the row tombstone, it will still screw up c1.
One possible solution I see would be to have specific row tombstones that only act on regular columns and others that only act on counter columns. Row deletion would then adds both kind of tombstone with the right timestamp each time. But we're talking internal format change, so that would postpone this to 1.0 at best (considering we want to do it).
Until that, we still have the possibility to disallow row deletion on mixed regular/counter column family.