If you are talking "cereal rye".......you do not need to worry as much about treating the water, although it certainly will not hurt. Cereal rye is fairly easy to kill.....especially so if it is mature (not growing fast). I sprayed my rye last week with 2,4-D(full rate), Prowl H2O(1/2 rate), and Scepter(1/2 rate). It is still green but stunted slightly. I will plant green and spray with glyphosate sometime after that. While I can't answer for NE, I don't think you need to get hung up so much on timing the spray for soybeans planted in rye.

For example....I sprayed my rye with a quart of glyphosate last year more than a month after planting, and it was dead the next week. those beans avg'd 52 bpa.....and that included several wet spots which drowned out.

post with pics from that saga:  http://talk.newagtalk.com/forums/thread-view.asp?tid=564249&posts=32#M4656764

and pics from a week later: http://talk.newagtalk.com/forums/thread-view.asp?tid=565391&posts=14#M4658353

Now.......if you are talking about Annual ryegrass (ARG).......then you need to definitely be treating you water (in my opinion) with the AMS and acidifier. I sprayed my ARG going to beans with the same residual mix as the rye, and will plant most of that green too, unless it looks like it will head out. Then I may terminate sooner.