This case is a bit different than the Haber process because these seeds are used to produce organisms that manufacture more of the seeds. If you are patenting the process to manufacture this type of GM soybean seed, won't it cover any process that is used to manufacture these seeds, including plants in a field? It is a tricky issue, and I don't know what the precedent is.

However, if they did patent the organism itself, or the result of the process (as e40 said in a sibling comment), then I am against this type patent.

Personally, I think IP law should be small and narrowly defined. I think that patents are valid when it is a scientific (ie non-trivial) process that has a limited duration.

EDIT: After thinking about it, I think the distinction comes down to this: are they selling it? if so they have no ownership rights on the next generation of seeds. Are they licensing it? If so, yes they do have ownership of the next generation of seeds. In that case, they are licensing to you a manufacturing process where you are allowed to sell the output, but you do not own the process itself.