I'd consider myself in pretty decent physical shape but I tend to run hot, often put some leg into it and consequently get a decent sweat on. Definitely go light. As you can see in my avatar I favour the sleeveless tops; they're cool and allow the armpits to breathe. Not wishing to start a debate but I don't wear a helmet on the commute either- reduces temperature for me. You can purchase (usually more expensive) super light ones though that are nice and breathable.
I'm not nearly organised enough for this, but you can always bring a full week's worth of work clothes on a Monday, keep a pair of shoes at work and travel very light for the coming week.
I shower first thing, then use a work shower upon arriving in. Being clean into your kit will reduce the potential of unwanted odor. You may do this already, but that's simply what I do; who doesn't enjoy singing in the shower? Twice in one morning is great.
Regarding clothes when at work, I agree with many of the others. Clean stuff each day, and even if they need to lurk under the desk they'll be fine for the journey home. They shouldn't smell too bad. If you're particularly self conscious perhaps wear a spare top until you get to your bike before switching into your commute one :-)