Virginia, I have nothing to add, I agree with both of the points you made, though very surprisingly, I'm just a tad less fatalistic than you in this case. There's a narrow way out reputationally speaking for Madame Secretary IMO and it's good governance coupled with spectacular Republican incompetence.
I do believe she has a shot at being looked at as a decent president, or at least not terrible, but she really has to deliver on substance. She has little charisma or natural charm like Obama and is already defined as a 'shady' character. If Republicans commit to obstructing Congress for her entire tenure as president, I do not think she will fare as well as Obama did. She really has to deliver on some of her campaign promises, and that will require Congressional action for many.
Republicans will probably continue to harm their brand by continued obstruction, but because of Trump, they will no doubt see this election as a fluke that was ruined by a selfish agitator and that all they need is a "true conservative" to run. This will give them the excuse they need to obstruct and demonize Hillary, so as to hopefully make sweeping gains in 2018 and also win the White House in 2020. This is the current GOP strategy - demonize and obstruct. They keep getting midterm blowouts and it only emboldens them to do whatever they have to for those sweet, sweet short term gains, regardless of bad they end up looking. I think the only way to change this is for them, in 2018, to have a 1998-style midterm instead of a 2014. It's like giving a dog a treat for crapping on the floor - Sure, it's bad, but the dog keeps getting rewarded for it and so it does it again hoping for the same results.
(sorry for rant lol)