Roger had an illness, it was more like Roger did not start the WAR (or could not for some reason, that's why he turned himself in to start the great era of pirates), he was waiting for the ONE (as WB said).
I think the Ancient Weapons are the argument the WG used to forbid research of the VC (we still dont know why the weapons existed in the first place). What they fear is the "True History" on the Ryo becomes known to the world.
Rayleigh's speech suggest otherwise. If that was the case, he'd have simply it was because of the illness but what he said implies they didn't know what they should do or weren't capable of doing for some other reason.
About the Ancient weapons, I hope there is something more than that. If there isn't, then the Rio Poneglyph probably has no real dangerous information, something someone could use to gain power since apparently all the texts about the weapons are on regular poneglyphs