Secondly, not everyone in a home run hitter. I know they impress the casual fan and that obviously if someone walked up and hit a home run every at bat, they'd be pretty impressive and score more runs than someone who did the same thing with singles. But honestly, Upton doesn't have to bash a million home runs to be good.
The areas where Upton beats Hamilton?
Try consistency for one. You linked their best months, I'll link their worst (I took out Hamilton's horrendous October, only because it was a meager three games):
Hamilton - .177/.253/.354, 4 HR, 8 BB, 21 SO, 10 R, 0 SB.
Upton - .242/.354/.379, 2 HR, 10 BB, 19 SO, 16 R, 3 SB.
In batting average, Hamilton's high month is a staggering .218 points in difference. When Hamilton is good, he's great, when he's bad though...he can cost his team games. What were our worst two months? Well, when Hamilton stunk in October, guess what? 0-3. And when he sucked for a full month in July? 9-14. The only month we couldn't manage at least a .500 record.
Next, Upton has the superior OBP, he gets on more. .355 to .354...it's not a huge difference, but consider this...think of the number of intentional walks Hamilton gets. Then consider the other stats you linked, including a month where Hamilton damn near batted .400. And yet, he loses to the guy who's best month was .060 points worse in batting average? On top of taking slightly more walks, Upton doesn't strike out as much. 162 SO for Hamilton to 121 for Upton.
You might say, well Hamilton bats more being the higher scoring offense... wrong, because Hamilton misses more games. Hamilton had 562 AB to Upton's 554. (Crazy thing I found here...not only are their ABs exactly 8 different, Hamilton has exactly 8 PAs on Upton, 636-628). And Upton has significantly more games played over Hamilton the last four years:
Year - Upton - Hamilton
2012 -150 - 148
2011 - 159 - 121
2010 - 133 - 133
2009 - 138 - 89
Total - 580 - 491
Oh and finally, there's a huge age difference...Hamilton turns 32 in May, Upton turns 26 (entering his prime) in August. I'm not saying Upton will walk in and replace Josh Hamilton. But he has notably more plate discipline, is far more consistent, plays more games, is younger and is entering his prime, unlike Hamilton who is exiting his.