The surviving Els aren't going anywhere, it is much cheaper to upkeep them or even upgrade them, than to build subway line from scratch.
For example; the Market-Frankford line was upgraded for mere ~ 1 billion dollars, much cheaper if it was built as subway and also much nicer than the Els around here.
Regarding employees, well, not everyone has to work for TA, if some can't work underground, they can find job elsewhere, its not that they are forced to work there.