Why is the Pardon controversial? Because Joe Arpaio is a controversial figure. He holds many views that are called racist. He was unapologetic in his actions, which makes him an unpopular person in the media. (this could be said to be objectively true as you will be hard pressed to find a positive Joe Arpaio story in NYT, LAT, CNN, NBC, etc. vs a host of negative stories. this is contrasted by the fact that the man was elected and re-elected many times)
Let's add to this that Arpaio is also an ardent supporter of President Trump, who is also unpopular in the media (again see above, Lots of negative stories, but the man won the election, winning the popular vote in many places where it was commonly thought by those same media outlets that he didn't have a chance)
Further adding to the controversy, the charge against Arpaio was contempt of court for failing to follow a court order. This is where we start to get in to several grey areas regarding the separation of powers. Contempt of Court is not something you get to have a jury of 12 type trial over. The judge says it, you go to jail. It can be used as a check against the executive because a judge can hit someone with an immediate, enforceable penalty. It's not often thought of that way, but it's there. Next we have the power of the Pardon, which is a check against both the legislative and the judiciary. If congress enacts an ordinance that is beyond the power of the veto, say against left handed basket weaving, the president could, in theory, pardon everyone convicted on such a ludicrous charge. He can also use it as a final check against that pesky Contempt of court thing.
Here is where it triggers all the sturm and drang. In many places, President Trump can do no right. "If he found a cure for cancer, he would be vilified for putting oncology doctors out of work". Likewise, Arpaio has been labeled a racist (regardless of evidence), a white supremacist (regardless of evidence), and is therefore "other". Anything positive between the two of them will immediately be attacked.
Now to address "contempt for the rule of law". This is pure opinion. It is a statement that has absolutely no basis in fact unless you can get in the head of the person and objectively examine their motives. We cannot, so anyone slinging that around just has an opinion, nothing more.
What is factual is that just as the court used a court order then a charge of contempt as a check on the executive (Sherrif Joe), another Executive (Trump) used a Pardon as a check against the Judiciary. The Court and president trump not only worked within the laws, but also the spirit of the laws and well within the spirit of the separation of powers. Very Very far from acting with "contempt" for the rule of law.
Sheriff Joe is the only one here who might be said to have acted with contempt for the law, and even that can be debated. He saw a bunch of laws regarding immigration that were getting twisted and ignored and as a duly elected officer of the law (executive) He went about enforcing them in the way he thought was best. His decisions were made with the goal of enforcing the rule of law, not in contempt of the rule of law. One could even make a case that Sheriff Joe was acting in the spirit of the Nuremburg War Trials, where "Just following orders" is no excuse, and one must follow their conscience instead.
The same reasoning that is being applied to Trump and Sheriff Joe to say that they have contempt for the rule of law can be applied to every single sanctuary city. It can be applied to those states who have "legalized" pot in spite of it being against federal law.
Finally, there has been talk about implications in a pardon over admission of guilt, or remorse, and so on. This one is fairly simple. Sherrif Joe, knows what he did. He does not deny that he did it. He thinks the Judge was incorrect about the law, therefore remorse and so on is unnecessary. This, at least, is pretty clear.
This is not an easy thing to reason through. In the end, unless you definitively know what was in the heads of Trump, Sheriff Joe, and the Judge who cited Sheriff Joe, all you can do is guess. All the Media Hype (both sides, mind you) is just that. Hype. If reporters are losing control of their bladders over this, they should be ignored at best, or at worst, cruelly mocked for their collective silliness.