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Whether you *will* be blackballed is a different question than whether you *should* be blackballed. Separating the two issues might be helpful. If you have principled views about trying to participate and help where you can, you should stick to your guns. More pragmatically, people’s reaction to your work in the administration will depend heavily on what work, exactly, you are doing. If you are in a front-line policy making position, and those policies are controversial, you should expect to take responsibility for the policies you help make. If you are, as you say, not at a “high level,” are doing your best to make government function in the public interest, and are not implementing policies you see as morally reprehensible, your engagement strategy seems reasonable.

For and with are very different. I would not recommend working for the Trump Admin. Working across party lines was one thing in prior administrations, Dem or Repub, but in my view this one is so fundamentally different. Initially there was some sense of do what one can from the inside. But Mattis and many other cases have shown the difficulties if not impossibility. Working "with" it, if you mean grants or informal relationships, may be different depending on what it is, who it is with, how confident one is of analytic honesty on their part.

There has long been a disconnect between academia and government. Some scholars have been able to bridge this gap by bringing to bear the insights from their research to inform government decision making. Others have chosen to use their research to be critical of government policies. In some ways, it is easier to be critical on the sidelines than it is to try to influence policy, but influencing policy can be a noble goal.

The Trump era seems uniquely polarized, but there are some precedents. For example, the 2003 Iraq war polarized the scholarly community. For those who worked with the Bush administration – think Jean Elshtain, who was established at the time – their reputations suffered. But Elshtain followed her convictions, and was willing to accept the fallout in doing so. That said, there were sometimes equally polarizing concerns in academia based on which camp one’s research fell into – the pro- or anti-Iraq war stance.

These are challenging contexts for young scholars to navigate, but ultimately I think it is important to let the scholarship do the talking. Focus on what your contribution is, and how it fits into broader debates beyond just the Trump administration. This is how young scholars navigated the Bush era, and did not let one or two publications define their career.

As for working for the administration itself, there is always a chance that this could have long-term consequences if one’s research is “polemical”. I would define polemical here as cutting against broader democratic ideals and serving the Trump administrations anti-women’s rights, anti-truth, anti-science, etc., agenda, but some might simply align polemical with conservative values.

That being said, to the extent that your research can serve as expertise in an administration that seems to eschew expertise, this could have a positive impact.

One additional point to consider: there are lots of people who currently work for the administration who may not agree with its policies: career diplomats, experts in the State Department or Department of Defense, just to name a few. Administrations come and go, but these professionals serve whatever administration is in power with their expertise. This could be one way of framing working with the current administration. To the extent that your research cuts across administrations – i.e. that it could have served the previous or might serve the next – offers another way of framing why you want to work with this administration.

A final thought: share your research broadly. Be careful of letting your work with the Trump administration define who you are as a scholar. Consider a broad research agenda, and work on developing a cross cutting network of scholars who comment on your work, give feedback, and want to read from it to learn from it.