Personally think that for development work, there's not too much a programmer can get from a GIS course, unless the course is run specifically for Computer Science students (which is rare). My learning (coming from a similar background to yours with lesser experience at the time) after enrolling in a Master's course was applied physics, spatial/locational modelling and statistical theory used in Remote Sensing amd Urban planning. It was all very interesting then, but I haven't used it since. Most of the work in GIS I have done has been standard IT work with basic GIS data model concepts involved. However, one of the biggest benifits of doing a Master's for me was learning how to write and present better and more confidently, which is a transferrable skill.
Questions you might want to ask yourself : Do you prefer open-source development or would you rather work with vendors such ESRI/Manifold/MapInfo etc.?
My personal choice for programming was open source tools and I picked up GIS specific Java tools such as JTS/GeoTools etc on my own and more recently GeoServer/gdal.
Do you prefer Desktop or web?
web development jobs are harder to find and the user base can be hard to please as they are used to highly interactive desktop apps
What field would you like to work in - government, military, environment?
By far the biggest advantages of a GIS career is opens up avenues into fields you might not have considered or had access to with just an IT background
Hope this helps