Hi D,
You may have taken her by surprise with such a personal question. It could be compared to a woman asking her male boss what she should do if her tampon or "maxi-pad" fails.
If your catheter leaks just throw a notebook over your lap and excuse yourself from the meeting and go to the bathroom. If you have a history of leakage you may want to "fix" the issue with a different style condom catheter that will offer you more confidence. Or intermittently catheterize more often during the day. And perhaps bring in a spare pair of pants if the leakage is that bad.
I think being terminated from your graduate internship may have been a bit drastic or even an over-reaction on your boss' part. I hope you asked her this in a private setting so you didn't embarrass her in front of anyone. Not everyone is as laid back about these issues as we SCI (and family and friends) have become. You need to "feel" people out before you start talking to them about personal SCI related issues especially in a professional setting or relationship.
Hopefully you can call her on the phone or set up a meeting, explain yourself and apologize for your indiscretion and get back into the graduate internship. Don't let it get out of hand by reporting it to her administrator before speaking with her about it first.
Good luck.