He also said it was an alternate timeline, a possible future.
That's not exactly what he said. He said: "This species has the technology that allows them to examine alternate timelines. They've seen this future and want to change the outcome". This means that by destroying the Spheres, Archer ensured that the war happened along the desired path. Daniels was trying to prevent the change of timeline, not change it himself. He deals with facts, not "what ifs". He shows Archer the path history should take, trying to convince him not to endanger that future.