I actually just read a book about Ike so this is timely.
Using the CIA to overthrow the democratically elected governments in Guatemala and Iran were probably worse than Operation Wetback. Guatemala was especially disgusting as it was heavily lobbied by United Fruit, who was going to lose a lot of money if the government wasn't overthrown, and it just so happened that they were in the pocket of tons of people in the White House - I mean John Foster Dulles was literally on their payroll when the operation went down. It also led to an explosion in CIA responsibilities and power, and we're still seeing the effects of the Iran overthrow today.
However, he didn't drop atomic bombs on Korea or China or Vietnam like a lot of people wanted to, and he ended the Korean war and kept us out of subsequent wars. When Britain, France, and Israel decided they would take over the Suez canal, he got then to back down by threatening to leverage US banks to devalue the British pound, which was already weak at the time. He sent federal troops to protect the Little Rock 9, desegregated the army, and appointed progressive federal judges that sped up desegregation in the south. He also actually curtailed military spending that was being clamored for, balanced the budget, and presided over a strong economy.
I don't think he chose his cabinet very well and relied too much on them. At times he let things he wanted to happen passively (not entirely unlike Obama) when he could (or should) have been more firm. Overall I'd say he was a pretty good president, though.