Establish branch office or private company

No doubt, you will wish to take legal advice but my gut feeling tells me that under nepali law, either the company you want to establish will be a commercial entity in nature or it will be a "non profit" organization. - One or the other -  Therefore, if the authorities deem that the company will be carrying on commercial activities like those you describe, the people at DOI (Department of Industry) will almost surely determine that the creation of a Private Limited Company is called for. If on the other hand, the purpose of the company is strictly "non profit", they will determine that you should form a Non-Governmental company - an NGO or "non profit" - And in that latter case,  DOI will not process your application but refer you to the SWC (Social Welfare Council) whose rules and regulations for NGOs are totally different. 
There's nothing easy about working in Nepal. I was never directly, myself, engaged in software development as such, but over the years I had occasion to commission a number of nepali firms to do software programs for our foreign group and internet system. Over time, I saw many IT and other well qualified people leave the country. The largest firm of them  all in Kathmandu had a central office in Thamel and at one time they had as many as 20 or more developers too. Finally, they shifted their whole operation to the USA.
Personally, I had occasion to work more directly with nepali webmasters and the like, and as the years passed, I noticed how more and more difficult it got to get qualified ones in Nepal. After 1-2 years of experience behind them, the temptation just became too great to want and leave the country and go abroad in search of better opportunity and higher pay. The best high tech man I ever had, who was a wizz, is now in Australia. As for those who remained in Nepal, in the majority of cases, they would work with us with up to say 2 years, get the experience and then leave us to form their own firm!
Whatever you decide, make sure the people you will want to work with have as high a command of the english language as possible. Technical ability and proficiency is one thing, but knowing english is a must in this field - And not just speaking ability, but the written language is vital, in my view particularly if your intention is to have them write or develop new programs for you in the international market.