It might help to know where you are in the world as you might want to consider different things depending on the schools. In the US, you can generally jump from a BSc to a PhD. In other places you generally need a master's degree.
How long is the MSc program and what will it cover? In some cases MSc coursework can be used towards PhD requirements, and so enrolling in a MSc program is like starting a PhD program. In other cases you might have to repeat the work - particularly if you enroll in a PhD at a different institution that insists you do it's coursework.
Do you have any kind of work lined up if you don't do the MSc this year? A lot of recent graduates are struggling to find work these days. If you end up unemployed for the first six months of your job search, how will that affect your student loan repayment? Conversely, if you have something that you could step into and start making good money at, you'd be in a good position moving into the PhD - not only repaying the loan, but possibly building up a nest egg so that your PhD years aren't quite a slime as they need to be. On top of that, it will give you some real world work experience that could come in handy after the PhD.
I don't know what you mean by "make up for" a 3.65 GPA. Sure, if you get a 4.00 in your MSc classes, it will look great on an PhD application. It probably won't elevate you to rock star status though. A lot can depend on the specific of the courses and program involved too.