I am a prosecutor or a deputy prosecutor.   Would pro bono work on sentence expungements be allowed under the Rules of Professional Responsibility? 

Probably yes, but you should check with your office policy before committing to such work. Prosecutors, including deputy prosecutors, have a duty of loyalty to the state of Indiana. Further, RPC 1.8(l) outlines limitations on part-time prosecutors and deputy prosecutors when they are representing private clients, which would include pro bono clients. However, the rule recognizes that upon express written limitation of responsibility to exclude prosecutorial authority in matters related to family law, a part-time deputy prosecutor may fully represent private clients in cases involving family law. If pursuing pro bono work as a prosecutor or deputy prosecutor, it would be wise to enter into a written agreement with your private client that notes the exclusion of the use of prosecutorial authority as a part of the private, pro bono representation.