I read a lot about how it is bad that the 49ers got to challenge a play after calling a time out. Let's consider how things would have played out if the 49ers had not been granted the time outs.
1. The officials would have missed a vikings fumble - this would have had a much greater impact on the game than an extra time out.
2. The clock would have still stopped regardless of whether it was a challenge or a regular time out.
3. The 49ers did get an extra clock stoppage since the fumble reversal did award them the ball with one time out, but if the officials had called the fumble correctly, they would have had the time out anyway.
So, regardless of the outcome, a correctly called game would have had the same impact as the 49ers challenging the 2 plays without a time out. If the 49ers had won, it would have been because they earned it, not because the officials made a mistake.
For what it is worth, I disagree with the current rule. If you have already called a time out, I don't see any reason why you can't also challenge the ruling on the field. The idea that you could lose 2 time outs on a single play is unreasonable.