Did Spider-Man filming halt so Tobey Maguire could bulk up?

Actually actors are supposed to do such things, like losing or getting weight to fit to the movie part. Tobey Maguire did this more than once. Here's the wiki part:

Maguire has been a vegetarian since 1992 and in 2009 became a vegan. He often makes changes in his diet to either gain or lose weight for movie roles; for example, he dramatically decreased his calorie intake for Seabiscuit followed by a rapid increase to regain weight for Spider-Man 2.

In the first Spider-Man movie as you said Peter Parker was a nerd student; so it wouldn't be realistic if that kind of student appeared with those muscles. So he had to workout a lot.

This article says that:

Maguire spent six months taking martial arts, weight training, and an intensive gymnastics programme in order to bulk up, look buff, and be able to match the lithe athleticism of Spider Man.

Maguire worked out a lot to get into that condition. On the DVD commentary, Raimi states that one of the first scenes shot was where Tobey takes off his shirt and is not in great shape while one of the last ones shot was the one in the mirror you are referring to.

In this article you can read exactly all the exercises he did. This is the diet:

Diet – Diet was an important part of the program. All fried nutrition was excluded to make way for healthy fruit like fruit, vegetables, whole grains, fresh meat low-fat milk and cottage cheese. Tobey drank about one gallon of water per day (3,7 liters) and eat every three hours.

I cannot find a YouTube video of this, but I saw the original audition Tobey Maguire did for Spider-Man. In the audition he took his shirt off to show how cut he was. This is what got him selected for the part. Here is an article online which talks about this. They didn't wait for him to bulk up, the scenes with him looking limp were CGI'd to make him look that way. http://www.eonline.com/news/59203/spider-man-s-shirtless-audition

I don't know how they handled it in this specific case, but keep in mind that usually scenes are not filmed in the chronological order they will end up in the movie. Reasons for this are mostly logistical and economical.

If you have several scenes in the same location throughout the movie, it is just practical to shoot them all at once. Also factors like weather, rent for equipment and locations, actor availability etc are relevant to this.

So while waiting for Maguire to "bulk up", they could easily shoot scenes that appear later in the movie where he either does not appear at all or where his body strength would not be visible because he is wearing clothes. Stopping the whole production for this seems unlikely.

I am pretty sure the scene of him looking weak and skinny was CG...

they didn't film him skinny then have him bulk up, they just used CG/airbrush to make him look that way

Actually the scene where we saw the skinny Peter Parker was not Tobey's body, it was his double actor's body. The next day where he was muscular is Tobey's body, before filming he worked out for 6 months and ate a balanced diet.

It's CGI. The nipples skinny Tobey has simply don't match the ones athletic Tobey has. You can work out and bulk up all you like, but that won't change the basic form, size, and colour of your nipples.