It will be tough, but you may be able to crack it with research and hard work.
Career focus issue: Either you changed plans or realized that an MBA will be much better. Serious research needed here: talk to people in the industry / position, talk to alumni from both programs and figure out the differences, etc. Changing plans is somehow more risky. Even when MBA grads do change all the time (I wonder how many actually do what they commit in their apps!) it will sound as if you change your mind about important things quite easily and adcoms won't like that.
Course waivers / 1 yr programs: try to focus on 1yr. programs that will waive courses (eg: Kellogg's). You may stand a better chance there as it might make more sense.
Stats: Make sure your stats look competitive. If they were competitive when you applied to MS, then even better. If not, retake GMAT and ace classes.
Other than that, i suggest you get as much help as you can.
Try to connect with alumni who have followed a similar path (i.e.: MS and then MBA) and get advice. I've heard they do exist in relevant (albeit far from majority) numbers.
To finalize, I would recommend an admissions consultant to help you on the strategy for your specific situation.
Hope it helps. Cheers.
L.