I believe that the btree structure will be different because it has to compare the column values differently.
Look at these two query plans:
mysql> explain select * from sometable where keycol = '3';
+----+-------------+-------+------+---------------+---------+---------+-------+------+--------------------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+------+---------------+---------+---------+-------+------+--------------------------+
| 1 | SIMPLE | pro | ref | PRIMARY | PRIMARY | 66 | const | 34 | Using where; Using index |
+----+-------------+-------+------+---------------+---------+---------+-------+------+--------------------------+
mysql> explain select * from sometable where binary keycol = '3';
+----+-------------+-------+-------+---------------+---------+---------+------+-------+--------------------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+-------+---------------+---------+---------+------+-------+--------------------------+
| 1 | SIMPLE | pro | index | NULL | PRIMARY | 132 | NULL | 14417 | Using where; Using index |
+----+-------------+-------+-------+---------------+---------+---------+------+-------+--------------------------+
If we change the collation for the comparison, suddenly it isn't even able to seek the index anymore and has to scan every row. The actual values stored in the index will be the same regardless of collation, for instance, because it will still return the value in its original casing regardless of whether it's using a case sensitive or case insensitive collation.
So lookups against a case insensitive collation should be a little less efficient.
However, I doubt you'd ever be able to notice the difference; note that MySQL makes everything case insensitive by default, so the impact can't be that terrible.
UPDATE:
You can see a similar effect for order by operations:
mysql> explain select * from sometable order by keycol collate latin1_general_cs;
+----+-------------+-------+-------+---------------+---------+---------+------+-------+-----------------------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+-------+---------------+---------+---------+------+-------+-----------------------------+
| 1 | SIMPLE | pro | index | NULL | PRIMARY | 132 | NULL | 14417 | Using index; Using filesort |
+----+-------------+-------+-------+---------------+---------+---------+------+-------+-----------------------------+
mysql> explain select * from sometable order by keycol ;
+----+-------------+-------+-------+---------------+---------+---------+------+-------+-------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+-------+---------------+---------+---------+------+-------+-------------+
| 1 | SIMPLE | pro | index | NULL | PRIMARY | 132 | NULL | 14417 | Using index |
+----+-------------+-------+-------+---------------+---------+---------+------+-------+-------------+
Note the extra 'filesort' stage required to execute the query. That means mysql is queuing up the result in a temporary buffer and sorting it itself using a quicksort in an extra stage, throwing out whatever the index order was. Using the original collation this step is uneccessary as mysql knows the order from index initially.