Trump has control over all the governments institution, he has the power to cut or increase funding to those institution. He who has the money has the control. Regardless of what scientist do, they still remain governments assets so they must follow direct orders from the president even if the orders seem weird.
Government scientists are being ordered not to talk about their research — and it’s only week one. When Trump assumed command of the federal government on Friday, he inherited thousands of civil servants who produce critically important research on disease threats, natural disasters, climate change, and so much more. This week, there are already several reports out that suggest major changes could be afoot.
While Trump does have control of the future of their projects and funding, he doesn't yet have enough control to make them lie and force the scientific community to endorse his worldview.
Given enough time and some firings (or worse to those who speak out) however he may get them to start espousing alternative facts and conclusions.
President Trump has his own opinions about science and climate change but he does not control government scientists. Yes, the president may get into heated discussions with the scientific community. However, Trump cannot control someone else. Government scientists are probably not that happy with the president's views on major issues but they can continue to speak out.
No, Trump does not control government scientists, because scientific research is still done by the scientific method and by peer review. Government scientists have a job to do, and a lot of science jobs in the government don't have anything to do with climate change or anything else politically related.