Two things. First, the modern Supreme Court was born out of a contentious conflict with the executive branch (
Marbury v. Madison - Wikipedia, the free encyclopedia). Presidents critique the courts all the time. Bush made the rallying cry of his 04 campaign pushing back against "activist judges" who, he claimed, didn't respect American tradition.
Second, unless I missed something Obama didn't criticize the legal reasoning underpinning the decision, only its implication, and this was in the context of proposing a new law to contain the fallout out of unfettered political contributions. Had he criticized them, given his previous employment as a constitutional law professor I don't think that would have been outrageous, but he didn't even do that.
GM, you've asserted that all this is "BAD" but you haven't told us why?