Hi there digital!
Welcome to scarleteen!
To answer your questions:
The chances of you having any sort of reaction to semen is highly unlikely, as it is a pretty inert mix of liquids, sperm, proteins, etc. I'll bet it had more to do with general irritation from initial sexual contact...
Consider the fact that this is first time you have had intercourse, and there is bound to be a little pain, swelling, and cramping...it sounds pretty normal, especially since it disappeared the next day. You also might not have been lubricated enough - a good lubricant like astroglide or KY jelly will take care of that. Lubricant is your friend.
However, I would urge you to use a condom to protect against STD's and STI's...unless the both of you have had full screenings, it is very easy to be unaware of an infection because many are asymptomatic...and, considering that you can get an STD or STI from many forms of contact (not just sexual - think of sharing towels in the locker room, or with friends) it is so much better to be safe than sorry.
In regards to the brown discharge...it sounds like a bit of "spotting," which is completely normal when you first go on the pill. Most women spot a bit for the first couple of months - definitely not a big deal. However, if you have any concerns, don't hesitate to talk to your doctor.
Hope this helps,
[This message has been edited by Lisa D (edited 05-13-2002).]