If you omit "in", you will have a grammatically correct sentence but it will not mean what you want it to mean. A preposition is needed, and the best one would be "to", not "in".
If you omit "in", "doing" becomes an adjective that modifies "point", so the meaning is nonsensical. To understand this better, consider the good sentence
"There is no couple dancing the cha-cha."
That makes sense because "dancing" does describe the couple. When you say "there is no point doing it that way" you are saying that there are no points that are doing it that way. It is absurd. Points never do things.
However, people do make this mistake frequently.