"Non-Hodgkins lymphoma" isn't one disease—it's many distinct conditions all lumped into one category. There are fast, aggressive NHLs and slow ("indolent"), treatable ones. The fact that your boss was out of work for a year during treatment means he had the former kind. Someone very close to me, on the other hand, has had an indolent NHL, the same kind Thompson has from what I've gathered, for over a year now, and she's missed a grand total of nine days of work.
Neither Thompson nor his doctors are lying or stupid. Indolent NHL is serious, yes, but it's highly treatable. There's no reason to believe that his lymphoma will prevent him from serving two full terms; in fact, odds are good NHL won't be what kills him when he does eventually die.
As the article states, FDT's marginal zone lymphoma is indolent (slow growing), is treatable, but not curable. His doctors have not been specific on his prognosis, but the literature states that marginal zone lymphoma (diagnosed in 2004), has a 5-year survival rate of 50-70%. The Bee touches lightly on this now, but if Fred should win the nomination the MSM will drum that figure into every person in the nation.