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How did Justice Thomas vote on this?

The case was in 1990, before Thomas was on the Court. However, here's some of what Thomas had to say in the followup case:

Not only did the court subscribe to a theory of injury that was predicated on black inferiority, it also married this concept of liability to our expansive approach to remedial powers. We have given the federal courts the freedom to use any measure necessary to reverse problems--such as racial isolation or low educational achievement-- that have proven stubbornly resistant to government policies. We have not permitted constitutional principles such as federalism or the separation of powers to stand in the way of our drive to reform the schools. Thus, the District Court here ordered massive expenditures by local and state authorities, without congressional or executive authorization and without any indication that such measures would attract whites back to KCMSD or raise KCMSD test scores. The time has come for us to put the genie back in the bottle.
The Constitution extends "[t]he judicial Power of the United States" to "all Cases, in Law and Equity, arising under this Constitution, the Laws of the United States, and Treaties made . . . under their Authority." Art. III, §§1, 2. I assume for purposes of this case that the remedial authority of the federal courts is inherent in the "judicial Power," as there is no general equitable remedial power expressly granted by the Constitution or by statute. As with any inherent judicial power, however, we ought to be reluctant to approve its aggressive or extravagant use, and instead we should exercise it in a manner consistent with our history and traditions.
Motivated by our worthy desire to eradicate segregation, however, we have disregarded this principle and given the courts unprecedented authority to shape a remedy in equity....
Our prior decision in this litigation suggested that we would approve the continued use of these expansive powers even when the need for their exercise had disappeared. In Missouri v. Jenkins, 495 U.S. 33 (1990) (Jenkins I), the District Court in this case had ordered an increase in local property taxes in order to fund its capital improvements plan. KCMSD, which had been ordered by the Court to finance 25% of the plan, could not pay its share due to state constitutional and statutory provisions placing a cap on property taxes. Although we held that principles of comity barred the District Court from imposing the tax increase itself (except as a last resort), we also concluded that the Court could order KCMSD to raise taxes, and could enjoin the state laws preventing KCMSD from doing so. With little analysis, we held that "a court order directing a local government body to levy its own taxes is plainly a judicial act within the power of a federal court."
Our willingness to unleash the federal equitable power has reached areas beyond school desegregation. Federal courts have used "structural injunctions," as they are known, not only to supervise our Nation's schools, but also to manage prisons, mental hospitals, and public housing. Judges have directed or managed the reconstruction of entire institutions and bureaucracies, with little regard for the inherent limitations on their authority.
Such extravagant uses of judicial power are at odds with the history and tradition of the equity power and the Framers' design. The available historical records suggest that the Framers did not intend federal equitable remedies to reach as broadly as we have permitted.
--snip--
Two clear restraints on the use of the equity power--federalism and the separation of powers--derive from the very form of our Government. Federal courts should pause before using their inherent equitable powers to intrude into the proper sphere of the States. We have long recognized that education is primarily a concern of local authorities. A structural reform decree eviscerates a State's discretionary authority over its own program and budgets and forces state officials to reallocate state resources and funds to the desegregation plan at the expense of other citizens, other government programs, and other institutions not represented in court. When District Courts seize complete control over the schools, they strip state and local governments of one of their most important governmental responsibilities, and thus deny their existence as independent governmental entities.
Federal courts do not possess the capabilities of state and local governments in addressing difficult educational problems. State and local school officials not only bear the responsibility for educational decisions, they also are better equipped than a single federal judge to make the day to day policy, curricular, and funding choices necessary to bring a school district into compliance with the Constitution. Federal courts simply cannot gather sufficient information to render an effective decree, have limited resources to induce compliance, and cannot seek political and public support for their remedies. When we presume to have the institutional ability to set effective educational, budgetary, or administrative policy, we transform the least dangerous branch into the most dangerous one.

Missouri v. Jenkins (1995)