I have not heard the Malaysian rolling "R" but, if it is like the Greek one, it makes speech harder to understand.
However, in Scotland most people use a rolling "R" so native English speakers have exactly the same problem with that (although to a lesser extent, since most of us are accustomed to hearing the Scottish accent).
So, without hearing you, all I can say is "it depends". If English people ask you to repeat, or look "blank" when you speak, then you may need to soften your "R". However, I think that intonation and stress are far more important factors.