If his advice was so mundane that everyone will do it anyway, then why was it stupid and objectionable? It can only be objectionable if you advocate that people vote against their own conscience, in which case your statement contradicts itself because you've plainly stated that "everyone votes their conscience."
I think this characterization of Cruz's comments might be valid in the abstract, but not if you consider it in the specific context in which it was made. The biggest story entering the Convention was the debate over addition of a "Conscience Clause", which would have permitted delegates whom voters bound to Trump to be unbound, and vote for someone other than Trump. That gave "conscience" a very particularized, specific meaning at the RNC -- not voting for Trump.
I personally took Cruz's deliberate inclusion and emphasis of that phrase to be meant applied in that particular context, and therefore, his "vote your conscience" urging was really a thinly- veiled urging to not vote for Trump. I believe that's why the reaction to his speech was what it was, and why he made the statements he did to his own constituents the following morning. He didn't even try to play the innocent card "Oh, I really didn't mean anything by it." He was pretty specific about not being a "lapdog", etc., and not giving his support to a man who had insulted him and his family.
Anyway, that's my reading of what happened. Obviously, others may interpret that differently.
I'll also say that as much as I dislike Trump, Cruz's speech still bothered me. But I admittedly was a pretty visceral "I won't vote for Trump" guy myself for quite awhile, and it took me time to get over that. Ted has recently come out and, while not endorsing Trump, has absolutely hammered Hillary. So maybe his (completely understandable) personal offense at what Trump said has waned a bit, and he's now going to work to see Hillary defeated.
In other words, I respect where he has ended up in this campaign, and why.