I'd use a pb_sv_load instead of exec command, but that's almost the same.
The thing is, if the pbsv.cfg is loaded after server.cfg, it could overwrite your custom commands...
What you should do is just run it via RCON, as you proposed, or via the PB WebTool.
Just put your custom commands in a file, then do pb_sv_load thatfile.cfg via RCON/WebTool.
If you just want to set up streaming to PBBans you can also do it only via RCON or the WebTool without touching the config files : http://www.pbbans.com/information.php?page=hubguide#rcon or http://www.pbbans.com/information.php?page=hubguide#webtool