I think this is a misunderstanding/misrepresentation of the argument. Following your logic, everyone criticising the Iraq war would be a hypocrite if they did not also oppose Congress' power to authorise wars.
Others are arguing that this executive order violates constitutional rights because it's awfully close to a religious test. Within that line of reasoning, there's no contradiction between opposing this order and not opposing Obama's, assuming those do not violate constitutional rights.
Others are arguing that this executive order violates constitutional rights because it's awfully close to a religious test. Within that line of reasoning, there's no contradiction between opposing this order and not opposing Obama's, assuming those do not violate constitutional rights.