We had these warnings prior to the first big api change, when the Magnemite eye warning first came out. I would ignore the warnings personally we basically had months of hassle free botting the last time we had these warnings, and they will disappear in a few weeks, with no bans. Basically we should assume Niantic are now focusing on big game changes, not bans.
If you remember we had the first big api change, people logged in the next day and the bots would not find pokemon and pokestops, then we had our first capcha. Then the old warning came up the same as the current one.