The glass ceiling mentioned by rpolicastro exists and is a very real barrier. In general, as an unspoken rule, you can't be the boss of people who have PhDs without a PhD (I'm sure there are exceptions especially if you put in the time).
That being said, I've met many people with a Master's or even just a Bachelor's that are as good if not better than people with PhD at bioinformatics.
The real question is 'how strong' and 'what' is your skill set. If you think you need an additional 3-7 years to hone and establish new skills in a more flexible environment then maybe a PhD is a good investment of time. If you already have those skills then you need to look at the cost-benefit for your self.
Unfortunately, many institutions will start you as an entry-level post-doc equivalent when you finish your PhD regardless of your skill set. The bioinformatics field is flooded with wet-lab scientists who switched to computational work in their final years/post-doc.
The job search is extremely dependent your proven experience and output (e.g. papers, projects, software) AND your ability to clearly illustrate that in your interview and CV - not to mention your raw interview skills. But also your own volition in not selling yourself short and knowing your worth.
Once you have a job you can rapidly climb the ladder (assuming you are in a work environment that allows for this) based on your ability. That being said maybe could you have already risen to that rank without the extra piece of paper.
It may be useful to clarify if your undergraduate degree is in biology (or related) or are you comp sci/math/statistics grad.
I have my undergrad degree in molecular bio from the same university I am currently getting my masters from.
You can go work in industry for a few years now and decide first hand. If you don't like it/feel constrained then switch back to a PhD program. With the experience you pick up you may be able to decide on a specific topic you find yourself interested in. In US you should be able to do that (may be difficult in other areas). While general advice is great (as you have seen in this thread), the specific situation you find yourself in, is what will be the ultimate decider.
It's not going to be the same answer for every country. I guess e.g. in the USA a PhD is important, whereas my experience in Finland is that nobody cares if you have a PhD. It's the industry experience that matters. Higher positions are generally filled with in-house promotions. Nobody is going to hire a PhD without industry experience to e.g. some senior position. Then on the other hand with entry positions a candidate with a PhD might seem too overqualified. Also, for management track an MBA is pretty much a must have..