Lions scrum-half Cusiter was taken to hospital with what looked like the latest in a sequence of shoulder injuries - while exciting young back-row star Beattie sustained a suspected ankle fracture.
Both departed during the opening 10 minutes and television replays suggested Cusiter could have been the victim of a late challenge by French-based Tongan forward Viliami Vaki.
Vaki appeared to drive Cusiter into the turf long after he had parted with the ball.
"I don't want to make any observations until I have watched the match on video," said Hadden.
"But I have to stress that losing two such important players so early in the game showed that we could make a seamless transition on the park.
"The fact that other players could come in so easily underlined the maturity in the squad.
"I feel heartbroken for Chris. He has had dreadful luck over the past couple of years."
Hadden is already resigned to being without captain Jason White and Ally Hogg long-term.
And Beattie's situation will be a major worry, not only for next weekend's encounter with Australia but the looming Six Nations campaign.
On his team's display, which yielded four tries before the break, but none in the second half Hadden added: "The guys have been asked to play at a certain intensity for three weeks and that is very hard to do.
"I was delighted with the first half performance. It was exceptional. The Pacific islanders are genetically programmed to play rugby, however we out-played them at their own game before half-time in attack.
"We then showed that quality in defence in the second half. You can't simply sit on a team like that for 80 minutes and the defence never lost its shape.
"That allowed us the luxury of practising a few things and we were always in control.
"The game we are building towards is a sophisticated one with lots of facets to it and I was so pleased with so much of it in the first half.
"The standard was so high that it was very hard to sustain."
Pacific Islands coach Pat Lam was full of praise for the Scots.
The Samoan, who had a spell on the home side's coaching staff, said: "I was very, very impressed with the way they are trying to play.
"It is the right way. It is an attacking game and you can see they have a lot of confidence.
"They are also a happy side, and that is so important. We took too much time to get up and running and let them do too much, too soon."
Scotland flanker Kelly Brown was voted man of the match - however, he also had mixed feelings as he looked ahead to Saturday's showdown with the Wallabies.
The Borders star said: "On the positive side, we have rattled up 70-odd points in the two autumn Tests so far, which is a pretty decent effort and one that has given us a lot of confidence.
"But on the other hand our performance in the second half proved we have a lot of work still to do."