First, do not use PuTTY. PuTTY is a GUI application intended for an interactive use. Use Plink, which is command-line/console equivalent of PuTTY intended for command automation. Being a console application, it has a standard output, which can be read in PHP (PuTTY as a GUI application does not have standard output).
In any case, there's no way to make PuTTY or Plink separate an output of command only (at least not from a command-line).
But what you can do, is to print some header/trailer to distinguish the start and end of the command output, like:
plink.exe -ssh pi@RasPiIP -pw raspberry "echo start-of-command && command && echo end-of-command"
And then in PHP, you can look for the start-of-command and end-of-command to identify what part of Plink output is really the command output