Trolley problem: 2035 version

[Anomalocaris]

Hypothetical scenario:

Congratulations!  Your DARPA funded project is a complete success!
You have discovered and fully characterized two neural subnets in the Allen catalog of the human brain.
1) A sub-ganglion whose configuration and activity fully characterize and implement gender beliefs and behavior.
2) A network which implements unique religious faith.

Fellow researcher, "Bob" has developed nano scale robots which are able to manipulate neurons at the molecular level.  Applying these to the above networks gives a capability of fully determining future beliefs and behavior.  Correctly used, this process is fully controlled and without deleterious side effects (impossible, I know, but this is my hypothetical.)  For example:
1) You can fully convert homosexual desire and behavior to stereotypically heterosexual.
2) You can convert any true believer in any religious faith to any other or remove any religious bias whatsoever, leaving the person atheist.

Is it ethically acceptable to use the nanobots to make the above modifications?

In most cases, no.  But never say never.

Let's say in 2036, a Mars sized rouge planet is detected heading towards earth on a collision course.   It is vastly beyond human capacity to avert the big splat.   There is nowhere near that we can escape to.   It take essentially the wholehearted effort of the whole mankind to build a generation ship that might allow a small human seedling population to depart on a long trip to survive.   That's humanity's only chance.  But half the population would rather pray for salvation at end time. I would say send in the 
Nanobots.

BTW, there is an answer to a more classical trolley car problem in there somewhere.