Don't throw it out, it will be fine. Depending on what minerals and additives are in your local water supply, it might be less than ideal, but you'll still get good soap out the other end.
Another option with chamomile is to infuse oil with it. I am curious to know how different the final products would be between these two methods. It sure would be quicker to steep in hot water rather than infuse room temp oil over a period of time!