Could this led to a retardation of the civil rights movement out of fear of setting precedent for the Philippines
Well, I am not sure; in fact, it might have also have the opposite result. Because by the late 1950s you would have the USA embroiled in a war on (at least typically) domestic soil. This would have set a precedent of a very large minority living in USA territory, whose members don't have political rights although they have the same responsibilities with full American citizens and who are subjected to discrimination and other unfair practices taking up arms against the government.
Now, when this uprising breaks out, there would be increased racial tensions inside the country, as Philippinos would be attacked by various "reputable" groups due to the "sedition". But it wouldn't take long for this situation to become worse, as groups such as the Klan could try to take advantage of this upheaval to become more aggressive against African-Americans, claiming that they were "the next Philippinos".
For its part, the US government would probably manage to draw the conclusion that the Philippines War had set a dangerous precedent, as it could give ideas to the various minorities if there wasn't significant change on the way they were treated. If the war also dragged on, this danger would become even greater. Thus, the US government might decide to push for civil rights legislation in the late 1950s, in order to prevent the threat from materialising.
But this itself would open a whole new can of worms, as the various segregationists would scream bloody murder and it might lead to the very situation the government wanted to avoid at all costs, with the South turning to something like a war - zone involving the Federal government on the one hand, the more militant African-American organisations on the other and Klansmen and other similar groups fighting against both. Add to the mix a USSR trying (or seeming to try) to take advantage of the US domestic distractions, things like all of Vietnam going communist after the departure of the French etc and the more rabid anticommunists in the USA would start claiming that the civil rights movement was indeed a communist plot to subvert the USA and this time, due to the ITTL situation ((much worse than OTL) domestic unrest, a protracted war in Asia sapping resources, the USSR adopting a more aggressive foreign policy etc.) could lead to these ideas gaining at least more traction than OTL, something that could result in some VERY GOOD THINGS.
Thus, a US government would have reasons to make such a decision and not make it.
(just my views; not sure if they are correct)