nisht: If there is any silliness , it was on the part of these Dayanim in Israel. It is actually not true that there was no kabolas ol mitzvos- a convenient lie. The fact that she was not following all mitzvos many years later has no connection to the original geirus. Please learn your halochos!
But to the main point: by freeing her without any get, they were making sure that any subsequent child was a mamzer. Better to accept the geirus-even if questionable because the results can be corrected than making more mamzerim, which cannot be corrected.