When my guts are bothering me, I first tend to put off eating breakfast for as long as possible--oftentimes not eating something until 11 or so.
Some people also try to wake up earlier so as to have time to do the bathroom thing and get through the worst of it before work. It also gives you time to take an imodium, anti-spasmodic or whatever it is that you use, and gives it time to kick in before work.
Is it possible that you could arrange to go into work an hour later and stay an hour later? Then you could continue to get up at the same time, and still have that extra time to get fixed. Make sure you tell them that you are having bowel problems in the mornings and that's why you've been running late, and why it might be a good thing to go ahead and make it a point to come in later. That way you have it on the record that you have an illness, which means they can't fire you under FMLA--not, at least, until you've racked up more than like 8 full work weeks worth of time in a year.