Yes, politics and morals can work against each other. The reason is because many times what is politically expedient is not morally correct. Often, politicians are too caught up in political games and they lack any real power to effectively change the status quo because there is too much political force being spent on maintaining the status quo.
It is my opinion that politics and morals work against each other because in order for someone to be a successful politician they must have the capacity to lie. Since lying is morally considered a wrongful act it cannot be ignored that politicians are sometimes expected to lie in order to achieve their goals. This makes them less moral.
Any time you are in politics in order to gain power or gain votes you must say one thing while you likely will take action the exact opposite way, I think if you are going into the political field you have to be ready to bend your morals in order to win.
Morality is the theory of what is right, without regard to the real world outcomes. Politics is the practice of governing in the real world where real world outcomes have meaning. Fortunes are lost, lives destroyed and people die when politics is ignored. Governments and people are corrupted and needless lives are lost and fortunes and growing economies destroyed when morality is abandoned. Politics is the testing to the morality that is the hypothesis. Without testing, governing will never become a science and progress towards the betterment of mankind will not occur.