It is about time a spade were called a spade. Freema has been sidelined because her performance lacked charisma. Partly this is not her fault as the Martha character was scripted as a generically feisty bore with a grating crush on the Doctor, however Freema clearly lacked the ability to make a silk purse out of a sow's ear and the production team want her out. However I suspect that there might be contractual reasons ewhy they can't just sack her. Also this might lead to her going to the press and 'dishing the dirt' , revealing behind-the-scenes rows etc. Therefore they've possibly palmed her off with the promise of 'new opportunities' in Torchwood in order to present a demotion as something else.
Obviously the above is speculation, however it is incisive speculation based on the glaringly obvious. Had Freema gained the confidence of the production team they would not be giving her a lesser role in the series. You don't demote successful people. They probably worked out very quickly in the shooting of the series 3 production blocks that she couldn't cut the mustard and so RTD rewrote the ending of 'Last of the Timelords' to have her leave. I'd guess that her contract was for two seasons or that they thought that sacking a companion would generate bad publicity. So they've possibly hauled her into the office and cut a deal: said words to the effect of: "Look Freema. We don't want to sack you. So here is option two: we give you a role in Torchwood and a few episodes of series 4 and you agree to accept this." Classic management tactic that.