regards
Simple, Congress has the power to mediate disputes between states of the Union, it's part of the Contract if you will. Seccession would be withdrawing from the Contract, due to previous violations by the other party or parties to it. Once a contract has been violated by one party, the other party has no obligation to uphold it. The North always wanted to have it's cake and eat it too. The Constitution also says that no state can be created out of another without that state's permission. West Virginia was created out of Virginia, without its permission. Virgina was still a state of the Union, if one also asserts that the Constitution forbides secession. You can't have Viginia be a state, and thus Lee and other be traitors, while at the same time it be OK to rip W. Va. away from Va.
An interesting question- if you are from Texas, as your nick implies, you might note the unusual conditions that Texas imposed on the USA prior to joining the union. One was the right to secede from the USA. r9etb has written a nice piece here but it ignores the context in which the union was formed. I do not think that any state was willing to concede its existence to the power of a federal authority.