My wife has this desire to be a SAHM. She's been trying her darndest to do while taking a full course load t school. She was doing great at it for the first few weeks but as that 1st trimester nausea and fatigue started settling in she started falling behind.

So as the loving husband I wish was more of the time I step in a do some house work. A lot of times I'm able to get it all done during one of her afternoon naps. (We have a 1 bedroom apartment and only a child in utero so its not too hard) and she feels guilty for not being able to do it.

So I tried the other approach and just let it pile up till she gets around to doing it. Then she gets upset with me for not helping her.

So my question for you is "where is the balance?" How do I help her keep the house clean without making her feel guilty?

There is no "balance." Let her feel guilty.

As you said, it's not terribly hard. And YOUR KID LIVES IN HER! Growing a human takes a toll on the body (as I understand it), and that's going to make it difficult to concentrate on school. When the baby arrives, concentrating on school(and/or anything else at all) is going to be even tougher...

If she starts in on 'feeling guilty,' just say, "this is the least I can do while you take care of yourself and our baby inside you." (And it is.) BE the husband/baby daddy that ALL of her friends are going to be jealous that they don't have.

Thank you for your input! That is what I've been trying to tell her.

"You are certainly doing a lot of work! You are carrying an entire child for me!"

This is an easy one.
Take mental notes of the easiest/less stressful things that need to be around the apt.
You take the more difficult of the chores and leave just a sprinkle of easy ones for her.
Example: 'Honey, you want to follow me with the swiffer and get these crumbs I'm wiping onto the floor?"
or maybe "My love, will you help me seperate the dry clean and gentle care clothes so I can knock out a couple loads? I dont want to ruin anything"

What ever the case is, you can include her on the chores so she doesnt get overwhelmed or feel like she's not doing her part.

...Once of MANY tricks up my sleeves