The war was not fought to free the slaves. The war was fought to prevent secession. The South was angry that the North did not return run-away slaves so southern states started to secede. This was 1861. The emancipation proclamation was in 1863.
The US government did return fugitive slaves. Per supreme court decisions, state officials had no role in the fugitive slave act.
Under the principle of federalism, state officials would have to use state procedures and follow state laws. The slave power didn’t care for free states requiring evidence, witnesses, and due process before an accused slave could be returned to his alleged master. Accordingly the state officials were not allowed to cooperate with slave catchers, and that duty fell to federal marshals.
After winning that court case, and with the later Dred Scott ruling that accused slaves had no access to federal courts to challenge the actions of slave catchers or federal marshals, there was no legitimate complaint that the slave power could make.