Why is it a big deal for non-combat items getting their raw materials from combat? Sourcing raw materials for craftables, plants, etc closes the loop, which improves player interactivity.
You don't have to kill stuff to get seeds... you can buy them from someone who did.
Dragon scales and high-end leathers come from monsters. I think having the resources drop off monsters was a great idea.
I really don't think seeds are going to be that expensive and the prices you can sell grown plants for will almost definitely give you a sizeable markup.
Also, the first reason given for why you can't cross polinate the new plants is that it would take a longer time to do that. Sure, they bumped back the publish, but wouldn't you rather the devs be done with this system and be able to allocate devs on other new content? I sure would.
I really think the devs made the best choice with how to do the plants. I actually prefer the way they're doing the seeds to the cross polination system. I think the new system encourages more people to give gardening a try because the system is generally simpler.