I would recommend to every rider that he/she practice braking while turning. It can be done, quite effectively, and without misadventures. I find that the Burgman (650 anyway) is especially adept at leaned-over braking, due to it's uncommon engine braking ability (which I happen to love, and use to it's greatest potential whenever possible).
Of course you won't brake as hard as you would if you were perpendicular to the roadway, but you can easily avoid most surprise obstacles with practice, and bring the bike to a complete stop in much less distance than you might expect.
The secret of course, is modulation. Learn how the brakes feel on every road surface you might encounter. (Start slow!) Yes, this means applying the brake (start with one wheel at a time - first the rear, then the front - then when you're comfortable, use both) until the tire begins to skid. (Again - start slow!) Then start practicing at relatively small angles.
The same holds for our wonderful engine braking. With proper throttle modulation, you won't even know it's there until you need it.
Honestly, I don't even think about what I'm doing when I brake anymore, unless it's a potential panic situation, and in those situations the most important thing is - don't panic. Practice = proficiency. Do it until it's mindless. 8)