Hashem told Moshe that Aharon should strike the ground. Rashi says the reason is because the ground had protected Moshe so it would be inappropriate for Moshe to strike the ground.
Was gratitude to an inanimate object so important that the leadership situation had to be altered, even temporarily, because of it? The plagues could have been considered such an important goal and need that perhaps that should have overridden the necessity of gratitude? I am sure, anyways, that had they been asked, the Nile and the ground would have agreed to allow Moshe to perform the plagues, considering how important the job was.
Hakaras Ha'Tov, gratitude, is not just "Thank you" and then you move on with your life. Hakaras HaTov is forever. Hakaras Ha'Tov creates a new relationship - it is something that cannot be ignored, even if there is somethin g important happening.
Moshe could not strike the ground, he could not strike the water, even though the purpose was very important. He could not do it because he had this unique relationship with those that had saved him.
If something needed to be done that is in contrast and conflict with that relationship, he could not just ignore the relationship and perform the act, an alternate method had to be found.