Hadley has a very elegant solution to do this inside data frames in his reshape package, using the function colsplit.
require(reshape)
> df <- data.frame(ID=11:13, FOO=c('a|b','b|c','x|y'))
> df
ID FOO
1 11 a|b
2 12 b|c
3 13 x|y
> df = transform(df, FOO = colsplit(FOO, split = "\\|", names = c('a', 'b')))
> df
ID FOO.a FOO.b
1 11 a b
2 12 b c
3 13 x y