It seems that Bnei Yisrael were acting in a totally irrational manner. Hurling stones is something one might do to punish someone or to protect oneself from a future aggressor. Yehoshua and Calev would not have elicited such behavior for either reason. They were righteous people who had never hurt anyone. What effect could they have on the future of Klal Yisrael? They were only two people.
This is, however, the nature of those who have alienated themselves from a Torah lifestyle. The diffidence that permeates their every action is manifest in their attitude towards their more observant counterpart. No one desires his conscience to demonstrate to him that his chosen way of life is doomed –spiritually, morally and physically. The truth hurts. When the pain becomes too great, he seeks to punish someone by throwing stones.
Bnei Yisrael feared going to Eretz Yisrael for a number of baseless reasons. The meraglim took advantage of these fears. Although they were only two individuals, Yehoshua and Calev represented a threat to their plans. When one who is unsure of himself attempts to convince others that he is acting appropriately, he cannot tolerate being accused of deception. When you consider the situation, it is easy to conceive that the leaders of the incursion wanted to stone Yehoshua and Calev.