Yes, someone on a president's team who has been compromised by the Russians would be a matter of concern. And the very first thing a legitimate counterintelligence or law enforcement agency would do is brief the president, reach a consensus on how to manage the investigation and safeguard information flows while the investigation is being completed.
I'm not an expert on these matters, but I've often wondered whether some of J. Edgar Hoover's tactics might have been explained by his suspicion that his chain of command was compromised. We know that the Roosevelt administration was compromised at very high levels. Truman was a strong anti-communist but there were Russian agents seeded across the government by the time he took over. Cleaning up the internal security mess -- that's assuming it was cleaned up, more or less -- was a long, messy process. And then there were the undercover communists and fellow travelers on Capitol Hill, both Members and staff. It's a fascinating story. The truth may never come out.
SCI is complicated, You think you know the white rats and the black rats, but they play the same games.
You move when political winds change in your favor, but try not to reveal your position.