But Townsend railed against the television match official and bunker review system after Afusipa Taumoepeau was only yellow carded for a head-high tackle on captain Jamie Ritchie.
Ritchie failed his head injury assessment and having already gone over the threshold of five previous concussions now faces 12 days on the sidelines in line with the return-to-play protocol.
It means the flanker will miss their must-win match against Romania in Lille on September 30, but should be back for a potential winner-takes-all clash against Ireland in the two sides' final pool game on October 7 in Paris.
"It's very disappointing that our captain, one of our key players, was hit in the head and was removed from the game," Townsend said.
The former Scotland and British and Irish Lions fly-half said he didn't understand how the review system was being operated.
"They're trying to look at ways of not giving a red card rather than referee what is a legal tackle... (it) should be a red card in my opinion.
"The TMO/bunker is not being delivered as I thought it would be, which is only (using it) if the referee at the time isn't sure if it's a yellow or red card."
"This is our showcase to show what's legal... I don't think it's good enough."
Turning to the result, with Scotland outscoring Tonga by seven tries to two, Townsend said the "game plan and intent and our contact work were really good".
"It's a six-day turnaround to Romania now and we know we've got to improve on this performance to get a bonus-point win. Then, we've got a shootout against Ireland if that's the case.
"We know we have to win our next two games."
Mixed emotions
Fly-half Finn Russell, who stood in as skipper after Ritchie's departure in the 34th minute, said the team had loved getting back on the pitch after two weeks off following their opening 18-3 defeat by South Africa.
"We prepared well and put out a decent enough performance. We're going to have to get better if want to stay in this competition after the group stages but we got what we needed tonight, which was a bonus-point win," he said.
Tonga skipper Ben Tameifuna said he had "mixed emotions".
"I'm very proud of the boys. The score doesn't reflect how much effort we put in this week," said the prop who scored a fine barn-storming individual try.
"Hopefully both teams have come away unscathed," he said of a no-holds barred clash that saw Tonga No 8 Vaea Fifita red-carded for a reckless ruck charge at the death.
The performance, he added, "goes to show where Tonga is at the moment. We can now see what it's like to be at the top level, so we just keep our heads down and keep chugging forward. Don't give up".
"We're trying to put our best foot forward but a couple of areas let us down," said Tameifuna.
"To give those opportunities to those dangerous backs they have, you can't afford to give those easy options."
Tonga coach Toutai Kefu, who won the 1999 World Cup as a player with Australia, said his team had "tried their hardest".
"Scotland are a good side," he said. "They controlled possession and territory and that was probably the difference."
Tonga, who lost their opener to Ireland 59-16, now face defending champions South Africa in Marseille on October 1 before finishing up against Romania a week later in Lille.
"It's another massive Test match for us. You don't play South Africa very often, but we'll turn up, bring our best and fire some shots next week," Kefu said of the Springboks game.
