First, disclaimer. I'm not sure I'm qualified to be giving anyone advice of this nature. But since you asked, here are my 2 cents.
The bottom line is that people do a PhD if they want to do research. Otherwise, probably not. I believe this is true in both academic and industry circles - if you want to do research type stuff, you need a PhD. I could be wrong about industry - if people know of counterexamples, please comment. So, a relevant question is whether you want to do research.
My experience is that in practical terms, at least in the applied sciences, research translates into more autonomy pursuing questions which you find interesting. In general, not having a PhD means less autonomy. Of course, having a PhD does not mean anything like total independence - there are always people you have to answer to. However, with just a Masters, you are much more likely to be taking direction from people in the choice of projects you pursue, and how you pursue them. You should try to figure out how happy you will be doing this. I used to think I would be Ok with that, and discovered later that I really wanted to be making my own decisions. So, you might think now that you are happy to do what you are told, you you may later discover that you do not consider these decisions that others make for you to be all that great. It really depends on your personality and inclinations.
It seems ridiculous that people will treat you differently on the basis of a piece of paper, but that is how human beings, at least the more bureaucratic variety, are constituted - they like to pigeonhole and put labels on people.
Having said all of the above, of course, if you do a Masters and then decide you want to do a PhD, you can always do it later, but I suppose you are trying to figure out the more efficient path to follow.
One fairly obvious question - is there some reason you can't go into the PhD program and leave with a Masters if you decide you don't want to do a PhD? I have done that (left a PhD program with a Masters), and it seems like a relatively common thing to do. I think that some Masters degrees do require a thesis, but others may just require coursework which you will be doing as part of the PhD program anyway. You can check with the programs you are considering what the rules for pursuing these options might be. If you could do this, it might be your best option. You can leave yourself some space and time for figuring out what you want to do, not pay lots of money in tuition, and not burn any bridges.
I have a PhD in Statistics, and know a fair amount about programming and related things (check my SE accounts), though my primary background is mathematical. I've also done some bioinformatics work. Given that, I'd say the comment by @Bitwise above is right on the money. With a big interdisciplinary field like bioinformatics, you need a lot of background and a fairly substantial and diverse skill set to get moving - cramming all that into a masters degree will be brutal unless you know a lot already. After a masters degree you might not know enough to do anything really interesting. Of course, you might be able to get an industry job where they will be willing to give you the space and time to learn more and develop. I don't have any experience of industry jobs; however from what I have heard, those sorts of conditions are more easily met in academia.
Also, personally I would not consider the cost of a MSc as a major factor when making such a decision, though of course it is a factor. I would think bigger picture, myself.