--- a/eclass/git-2.eclass	
+++ a/eclass/git-2.eclass	
@@ -119,6 +119,14 @@ DEPEND="dev-vcs/git"
 # non bare repositories. This is useful if you can't operate with bare
 # checkouts for some reason.
 
+# @ECLASS-VARIABLE: EGIT_FORCE_FETCH_UPDATE
+# @DEFAULT_UNSET
+# @DESCRIPTION:
+# If non-empty this variable forces the git update repo to use git fetch
+# no matter the repo type (bare/non bare). This is useful if you are using
+# a non bare repo and the remote tends to rebase the tracked branch with
+# conflicting commits, as git pull doesn't handle that situation gracefully.
+
 # @ECLASS-VARIABLE: EGIT_NOUNPACK
 # @DEFAULT_UNSET
 # @DESCRIPTION:
@@ -536,7 +544,7 @@ git-2_migrate_repository() {
 	fi
 
 	# set various options to work with both targets
-	if [[ ${bare} ]]; then
+	if [[ ${bare} || -n ${EGIT_FORCE_FETCH_UPDATE} ]]; then
 		debug-print "${FUNCNAME}: working in bare repository for \"${EGIT_DIR}\""
 		EGIT_LOCAL_OPTIONS+="${EGIT_OPTIONS} --bare"
 		MOVE_COMMAND="git clone -l -s -n ${EGIT_DIR// /\\ }"