As mentioned in my comment, the easiest way I can think of would be to add a thousands option to the argument list of print.default and an if() statement in the body.
print.default <- function (x, digits = NULL, quote = TRUE, na.print = NULL, print.gap = NULL, 
                           right = FALSE, max = NULL, useSource = TRUE, thousands = TRUE, ...) 
{
    noOpt <- missing(digits) && missing(quote) && missing(na.print) && 
        missing(print.gap) && missing(right) && missing(max) && 
        missing(useSource) && missing(...)
    if(thousands) {
        return(formatC(x, format="d", big.mark=","))
    }
    .Internal(print.default(x, digits, quote, na.print, print.gap, 
                            right, max, useSource, noOpt))
}
Now we will have to wrap with print, but it works well.
print(1:10 * 100000)
# [1] "100,000"   "200,000"   "300,000"   "400,000"   "500,000"   "600,000"  
# [7] "700,000"   "800,000"   "900,000"   "1,000,000"
print(1:10 * 100000, thousands=FALSE)
# [1] 1e+05 2e+05 3e+05 4e+05 5e+05 6e+05 7e+05 8e+05 9e+05 1e+06