From Wikipedia:
"The Second Samoan Civil War was a conflict that reached a head in 1898 when Germany, the United Kingdom, and the United States were locked in dispute over who should have control over the Samoa Islands. The Siege of Apia occurred during the Second Samoan Civil War in March 1899 at Apia. Samoan forces loyal to Prince Tanu were besieged by a larger force of Samoan rebels loyal to Mata'afa Iosefo. Supporting Prince Tanu were landing parties from four British and American warships. Over the course of several days of fighting, the Samoan rebels were defeated.
American and British warships shelled Apia on 15 March 1899; including the USS Philadelphia. Germany, the United Kingdom and the United States quickly resolved to end the hostilities and partitioned the island chain at the Tripartite Convention of 1899, signed at Washington on 2 December 1899 with ratifications exchanged on 16 February 1900."
So it seems like butterflying away the Second Samoan Civil War would make partition less likely.