The clash between Beerus and Goku was not what created those shockwaves that the Grand Supreme Kai and Whis themselves stated would destroy the universe. I don’t think you’re denying Whis’s words, are you? Whis is more than a reliable source; he has vast knowledge and experience, and we all know this, and he is the strongest in Universe 7. What caused those waves was the collision of punches between Beerus and Goku—not a general clash in direct combat, but specifically the punches themselves.
The collision between Goku’s punch and Beerus’s punch generated those waves, and if those punches had continued, the entire universe would have been destroyed into nothingness. This is exactly what Whis said and what the Grand Supreme Kai mentioned. However, Goku then realized the danger of the situation, so he adjusted the trajectory of his punch to match Beerus’s punch and learned how to focus the power and angle of his strike, which caused the waves to stop.
Those waves did in fact destroy distant planets, but if they had continued, they would have destroyed the entire universe (if they had continued). These waves were destroying planets that were extremely far away, which means the damage was not limited to the point of impact, but occurred on a very large, distant scale. But if Goku had continued throwing those punches, the entire universe would have been destroyed into nothingness—however, as I said, he learned how to regulate and control them.