What you're proposing is an enormous increase in complexity of equipment, which would have an impact not only on price but also reliability of the space segment. A "bent-pipe" space segment with minimal control logic is a well-established norm in communications satellites for a few reasons, ranging from reliability to making it possible to use existing transponders with future modes. Even still, more and more communications satellites use digital transponders that can authenticate source messages, and so this issue mostly exists with legacy satellites that can't be retrofitted.
Besides, there's not really much motivation to mitigate this problem. First, pirate satellite communications by SARSAT transponders are rare compared to other satellite systems very popular with pirates like legacy US Navy communications satellites. Second, satellite piracy isn't that popular overall. Mitigating the ability of criminal organizations to communicate this way would require taking down a lot of different satellite systems, and then they would just fall back to HF radio, which is already the more popular approach. It's doubtful there would be any major reductions in crime and the type of crime that seems to motivate the most use of satellite piracy---unlicensed fishing near the Phillipines---isn't super high on the list of international priorities.
Besides, there's not really much motivation to mitigate this problem. First, pirate satellite communications by SARSAT transponders are rare compared to other satellite systems very popular with pirates like legacy US Navy communications satellites. Second, satellite piracy isn't that popular overall. Mitigating the ability of criminal organizations to communicate this way would require taking down a lot of different satellite systems, and then they would just fall back to HF radio, which is already the more popular approach. It's doubtful there would be any major reductions in crime and the type of crime that seems to motivate the most use of satellite piracy---unlicensed fishing near the Phillipines---isn't super high on the list of international priorities.