Fridge Brilliance: Ok, it does seem a bit weird that people created the god Eesa and decided to kill her, which will likely fall in the situation of needing a god AGAIN years to come, but consider this; it draws parallels to any sort of dominating religion. People create gods and faith as a way of letting them decide their life for them, so they don't have to worry and just ask the God what to do. In this case, decide on Laws between Destruction and Creation. However, people like Weiss wised up realizing people put TOO MUCH faith in the gods to the point it dominates their life, like Olquina and Turemelia (hence his drastic means). Remember Hosea? He RULED the normally democratic republic through Imaginal religion. This game may have not gotten the point clearly across, but it's basically saying your free will is more important than the voice of religion always tying you down, and there shouldn't be so much dependency on them. Even Eesa doubted if she was truly needed if people CAN live without gods, but only ignored that epiphany when she knew she would cease to exist, sad as it is.
Fridge Logic: L'Arc's eventual wish is for humans to life without the gods, as they did before they came into being... except, it was because humanity lacked the gods in the first place that they came into existence. So, who's to say that more of them won't appear in the future?
They won't. God's in this game are beings touted as such by humanity when they couldn't bear to make their own choices. Every God in this game is only referred to as such because humanity chose to worship it as one. Eesa—the Singing Stone—was discovered by the Twelve Heroes, and it was their choice to make it humanity's God, even though they all had their own reservations about it. As some characters so bluntly put it, Eesa's just a rock. A really unique and powerful one, but a rock nonetheless, and the same goes for Real and Imaginal. At the end, Eesa reveals her own misgivings about her ability to lead the people who entrusted themselves to her, and supports the heroes' decision to let humanity take responsibility for its future. So long as humans are able to think for themselves and take responsibility for their actions, "Gods" shouldn't appear ever again. L'Arc, Ryfia, probably Cecille and the other's descendants are there to make sure of it, remember?