The owner of the Haber Process patent has no say in what the ammonia gets used for after they have sold said ammonia. Nor should they.
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.
I like that distinction between selling and licensing. It clears things up a bit and also exposes the ridiculous/terrifying consequences of being able to license lifeforms.
We're certainly not far away from modification of humans, at least in small ways, so we better have it figured out by then. If you, through some patented process, gave your children some genes for disease resistance the legal framework in place for agriculture would have the preposterous effect of giving patent holders control over how they were allowed to reproduce. Bit of hyperbolic example surely, but still an instructive one IMO.