The Treaty was ratified by the Senate in the closing days of the 55th Congress (February 1899). The 56th Congress would be much more Republican.
http://www.senate.gov/pagelayout/history/one_item_and_teasers/partydiv.htm
Given the change from 44 Republicans in the 55th Congress to 53 (not counting Silver Republicans) in the 56th, it seems very likely that the
Treaty would pass the 56th Congress even if narrowly rejected in the 55th.
It is true that even in the new Congress a unified front by all Democrats and Populists could defeat the treaty. But such unity was extremely unlikely--even if Bryan had come out against the Treaty. (Eight of the ten Democrats who in OTL voted for the Treaty announced they would do so before Bryan came out for ratification.)