Your complaint is exactly mine, except that I eventually gave up and just started reading novels on it.
You have a few options, all of them begin with rooting the device.
To the best of my knowledge, there are four PDF readers for the 1st edition nook: the stock one, djvudroid, apdf(viewer), and orion. Basically, the ideal situation is that you can display your textbook in landscape, without margins, zoomed to fit width, while preserving structure. The stock reader mangles PDFs unless they're entirely reflowable text, so that's out. apdf might work, but it only supports a limited set of zoom ratios, so you can't zoom-to-fit. Panning is also awkward. I never managed to get djvudroid to build, and I only found out about orion a few days ago and haven't tried it.
Even if you find a good reader, you'll probably have to preprocess your PDFs to crop the margins-there are a variety of programs that do this automatically, and none of them work very well.
Of course, it's relatively easy to write a PDF viewer that does the right thing for the 1st edition nook if you already have a PDF rendering library and logic for display to eink (and you know how to write to a quirky obsolete version of android!). Unfortunately, I've just never been motivated enough to work on one. No one else has either, because as soon as the NST came out, software development for the 1st edition nook completely stopped.
If you decide to buy a NST, the situation, surprisingly, isn't completely better. The "best" pdf reader for the NST is probably EzPDF, and it leaves a lot to be desired (it plainly was not written with e-ink in mind). Here writing your own gets a little easier, but I just wanted to read some textbooks, not learn how to develop for yet another platform.
The other reply you got isn't entirely off-base: you'll find that even if you manage to arrange things perfectly, a lot of books remain really inconvenient to read straight through. Unfortunately, the e-textbook market is going nowhere, LCD tablets are terrible for reading, large e-ink devices are rare and costly, and I guess not enough people with nooks are interested to fix the problem to the extent it can be fixed.