It would help if you post some example KOs here. Use keggrest and user manual here. Sequence object is biostrings. You can write them to hdd in fasta format using biostrings package (writeXStringSet function). Try below example code and example kegg IDs are taken from manual::

library(KEGGREST)
test.seq=keggGet(c("hsa:10458", "ece:Z5100"), "ntseq")
library(Biostrings)
writeXStringSet(test.seq,"temp.fa", format = "fasta")