Why would Obama's prospects have any kind of significant effect on kratom's legality? Congress writes legislation. Obama could veto kratom prohibition, I guess, but he hasn't shown himself to be more pro-drug than any other recent president.
As a senatorial candidate, Obama advocated marijuana decriminalization, a position he renounced when he ran for president. As a presidential candidate, he said he would end the DEA's medical marijuana raids, a promise he broke after he was elected. So far he has waged the war on drugs, which he once called an "utter failure," in pretty much the same manner as his predecessor, only with more money. The one substantial improvement in federal drug policy since Obama took office is crack sentencing reform, which he supported. But that change was in the works for years and had already attracted support from most Republicans, including George Bush.
I would expect that kratom would be illegalized via a random, trivial action of some government agency, not something at the executive level. Broadly, though there are many, many scenarios where kratom could be illegalized under Obama, there are more under a Republican president. For one reason, it is at least possible that national drug prohibition could end during a second term of Obama where that is more or less impossible under a Republic executive.