With minimal rewriting, you can use simply bad or the more hoity-toity prove disadvantageous or perhaps setback (or obstacle, delay, disadvantage) in your examples. In following, the first right arrow (→) sets off examples rewritten with bad or prove disadvantageous, and the second arrow sets off more-thorough rewrites.
Example: "The economy has been a big ? for our organization" → "The economy has been bad for our organization" or "The economy has proven disadvantageous for our organization"→ "The economy sandbagged our organization" or "The economy dealt our organization mortal wounds."
Example: "One ? to the driver was that his tires were going flat" → "A setback for the driver was that his tires were going flat" or "It was bad for the driver that his tires were flat" → "The driver's ontime record collapsed as his tires went flat."
Example: "Writing them an angry letter would be a big ? for our group" → "Writing them an angry letter would be a serious setback for our group" "Writing them an angry letter would prove disadvantageous for our group" → "Writing them an angry letter would provide our group tremendous spiritual comfort and no end of grief."
Comment: I suggest posting questions like yours in writers.stackexchange, suitably revised to ask about how best to phrase your examples. Trying to shoehorn a single word into these disparate slots is a mistake; your effort would be better spent rewriting the sentences in less-clumsy forms.