Because he would be found innocent by a Virgina jury (which Johnson feared) or because his case for secession would be upheld?
The first reason is reasonable, the second one isn't.
Because if the secession of Virginia from the Union was not lawful, than the secession of several western Virginia counties from Virginia [peacably and de jure, by the way] to become the Unionist state of West Virginia was not constitutionally permissible:
U.S. Constitution, Article IV, Section 3:
Clause 1: New States may be admitted by the Congress into this Union; but no new State shall be formed or erected within the Jurisdiction of any other State; nor any State be formed by the Junction of two or more States, or Parts of States, without the Consent of the Legislatures of the States concerned as well as of the Congress.
If the secession of the south was not lawful, than the creation of West Virginia was an extraconstitutional, impeachable act by an out of control dictator.
Interesting that you blame it on Lincoln when the President has no constitutional role in creating a state.
West Virginia was created when a anti-secession segment of the Virginia legislature broke away and petitioned the U.S. Congress to be recognized as the legitimate Virginia legislature. This was done and a loyal governor, senator, and congressmen were chosen and sent to Washington. This legislature voted to partition Virginia into two states and requested permission from Congress to do so. Congress granted this permission and West Virginia was formed and later admitted as a state. All proper and within the bounds of the Constitution. Was it legal? There is some question as to whether the Virginia constitution was violated in terms of quorum for doing business, but that would be a matter for the courts to decide. But as to your claim that it was unconstitutional or impeachable. Nonsense.
Admittingly W.Virgina did raise some problems.
However, since Virgina was in revolt, those who were loyal to the Union needed to be protected.
What W.Virgina does show is the logical outcome of allowing secession as a means of dealing with political disagreements.