Rather than expresses a preference for the first option over the second but does not exclude it from consideration.
Instead of expresses the choice of the first option to the exclusion of the second. For example someone might say:
"As a general rule I would take the bus to work rather than drive."
However if there was disruption to the bus service or the person had a site visit to do on a specific day they might say
"Today I will drive to work instead of taking the bus"
Having made a decision as to which mode of transport to use on a particular day the other is excluded, you can't travel to work by car and bus simultaneously. Also once you have left the car at home you can't use it to get back and if you drive to work you will have to drive home unless you leave the car overnight for some reason.
In the case of your manager the appropriate phrase is probably rather than since an emphasis on efficiency doesn't normally preclude expansion. However there are situations where instead of would be appropriate. An example would be "Our manager wants us to concentrate on the details of the paperwork instead of providing a good service to the customers". This implies that the manager's priorties are wrong and that his insistance on minutely accurate paperwork is interfering with the core function of the business.
The other two phrases do not fit into the sentence as it stands but could be used with more explanation. For example "...although he is still interested in expansion" and "...even if it inhibits our expansion"