Seriously, it would be a pain in the ass to balance that.
You would have to decide whether shots/projectiles can pass through the portal. Also if both teams can use it, or the won team only. That would actually make it more a two-way teleporter than a portal (noticed how you can't look through the portal in the demo video? Could be the developer is rather imitating the effect than using the portal technology ...).
All maps would have to be re-edited to define materials to put a portal on (or not), which unlike
Portal would not be intuitive at all.
Not to mention that indeed you could reach spots the map maker never intended to be reached, potentially disclosing facades and half-built sections.
Also, how many portal guns would be in use? Only one per team? Only a certain class? (But what if 10 people would play that class?) Or could every player carry a portal gun? Of course that would make for a highly dynamic game

If anything something like that would have to be a separate MOD, with redefined classes and/or weaponry and adapted maps (preferably indoors, otherwise the use of the portal gun would be somewhat limited).