Transfering between graduate programs at the same university
Programme transfers are pretty common and most modern universities have established procedures in place to allow this to happen. At my university -- a research-intensive one in the UK -- this would only be allowed if you meet the following conditions. For the sake of clarity, I will call the programme from which you wish to transfer programme A and the programme into which you wish to transfer programme B.


You meet the entry criteria of programme B. In most cases in which programmes A and B are related, this is not a problem. The greater the difference, the smaller the likelihood that these criteria will be met. The most common cause of grief in our experience is potentially different English language thresholds. For example, programme A might have an IELTS requirement of 6.5 while programme B might require IELTS 7.0.
You have no outstanding incomplete requirements in programme B.
The programme director of programme B is willing to release you. This is relatively easy because most programme directors have no desire to keep anyone who doesn't want to be there.
The programme director of programme A is willing to accept you. The programme director will want to review your academic qualifications and performance. This review may involve an interview or skills demonstration. For example, you might need to demonstrate facility with a piece of lab instrumentation or software.


If you meet all four criteria, then the question becomes about inter-programme credits. Depending on the coverage of the taught components of programme A and its overlap with programme B, you may be asked to take courses to make up the taught credit load for programme B. 

Finally, you will be asked to choose an academic supervisor who will oversee the research component of your degree.

If you want to transfer out of a programme, I suggest that you do so now. Unlike PhD programmes, master's degrees are churn out students at a much faster pace. Thus, the academic supervisor you have in your original programme isn't likely to have developed a strong working relationship with you. I wouldn't overthink the issue that you are inconveniencing him or her much. This happens quite often and is the reason that policies are in place. 

Finally, if you are professional about your reasons for departure and your approach to the process, there is no reason why you will be "blacklisted", should you then try for a PhD or post-doc position in your original programme.

Good luck to you.