The Jaeger's brain capacity is too large for a single human to control, therefore they need two. I don't recall it's ever specified how the division of labor occurs (who does what), but it would even make more sense that neither operator knows which part they are controlling.
For the example's sake, let's assume the left operator (A) controls the left side of the Jaeger, and the right operator (B) controls the right side.
If they want the Jaeger to start walking forwards, it needs to put one leg in front of the other. But if A wants to start by putting the left leg forwards, and B wants to start by putting the right leg forwards, then the Jaeger's movement will be erratic and the Jaeger will fall down.
The operators need to be in agreement about the Jaeger's moves, or otherwise they will send mixed signals.
A simple(r) solution would be to have A only move his left limbs, and have B move his right limbs. However, this means that both operators are doing their own thing, and are not able to consider whether their actions conflict with the other's actions.
If operator A (as a human) is incapable of walking by moving both legs forward at the same time, he will notice that when he tries to perform this maneuver. And therefore, he won't accidentally make the Jaeger do something that he can't do himself.
So instead the operators mimic eachother's moves. Even though A's right limbs do not control anything, he still moves them. Because he is now mimicking the whole Jaeger instead of only his part, he is always able to consider whether his own actions work together with the actions of their colleague.
There are two possibilities:
- A's movement with his right limbs is free. He can do what he want, because he's not controlling anything with it anyway. This means that he chooses to move his right limbs the same way that B does.
- A's movement with his right limbs is not free. The Jaeger forces him to make the same movements as B, because B is controlling the right limbs.
It's been a while since I watched the movie, but I seem to remember a scene where the operators went out of sync and messed up (not the protagonist and his brother). This means that the operators have enough freedom to choose to not mimic the other; because otherwise this scene could not have occurred.
This is why operators need to have a close mental connection in order to work together seamlessly. Although it would be possible to have two foreign operators verbally discuss how they are going to walk before attempting to do so; there is no time for discussion when you're in the middle of combat and one of them needs to make a snap decision (e.g. dodging).
Jaeger pilots are therefore expected to know what the other is thinking, so that they can work together well even if under considerable time pressure. They understand one another, and therefore don't waste time disagreeing or trying to think of soemthing together.
So to answer your question: It seems to me that Jaeger pilots could move freely and are not being moved around by the Jaeger; but they should perform the same movement anyway, to prevent them going out of sync or making separate decisions that conflict.