If I understand the problem correctly (radial or axial holes?) I would agree with the two V block solution. Just be sure that at least one block is fully clamped before you unclamp/move the other one. In this case, as the rod to be drilled is longer than the table, this will have to be done in several (2 or 3) moves but should still work.
By the way, using two V blocks in this way is a useful method to drill parallel holes at regularly spaced intervals in rod. Drill the first hole using a fixed V block (e.g. it's clamped to the drill table), clamp a second block to the rod at the required distance from the first (a spacer can be used), unclamp the first block from the material (but don't move the block on the table) and slide the second block up to it, which will also slide the rod the required distance. Drill your next hole and repeat as required. As highlighted above, at least one V block is always clamped to the work piece at all times…
A very simple idea but it works well and is perhaps not as obvious as it seems.
Regards,
IanT