Either there were correct and incorrect reasons for someone to become circumcised and Paul was only speaking against the incorrect reasons, or according to Galatians 5:2, Christ is of no value to roughly 80% of the men in the US and Paul caused Christ to be of no value to Timothy when he had him circumcised (Acts 16:3). In Acts 15:1, they were wanting to require all Gentiles to become circumcised in order to become saved, however, that was never the purpose for which God commanded circumcision, so the problem was that circumcision was being used for a man-made purpose that went above and beyond the purpose for which God commanded it. So the Jerusalem Council upheld the Mosaic Law by correct ruling against that requirement, and a ruling against requiring something that God never commanded should not be mistaken as being a ruling against requiring what God has commanded as if the Jerusalem Council had the authority to countermand God. So Paul was only speaking against incorrect reasons for becoming circumcised, not against what God has commanded.
Paul said that circumcision has no value, that what matters is obeying the commandments of God (1 Corinthians 7:19), that circumcision has much value in every way (Romans 3:1-2), and that circumcision has value if we obey God's law (Romans 2:25), so the issue is that circumcision has no inherent value and that its value is entirely derived from whether we obey the Mosaic Law. In Isaiah 45:17, it says that all Israel will be saved, so the problem was that some Jews were considering themselves to have a higher status than Gentiles and were considering themselves to be saved simply because they were circumcised after they were born, but even Jews need to be born again. In Romans 2:26, the way to recognize that a Gentile has a circumcised heart is by seeing their obedience to the Mosaic Law, which is the same way to tell for a Jew (Deuteronomy 10:12-16, 30:6), while the way to recognize that someone has an uncircumcised heart is by their refusal to submit to the Mosaic Law (Jeremiah 9:26, Acts 7:51-53). So Paul was not contrasting God's commands with God's commands.