Making the Astral Plane a High-level Destination
The Astral Plane is already a mid-level destination. The chart Astral Plane Encounters (DMG 154) lists the minimum Astral Plane encounter as EL 8 with 1 noble djinn (MM 114-5) (perhaps accompanied and captured--so it can grant wishes--by some insignificant-to-the-EL githyanki who lost their mid-level githyanki during their encounter with the djinn) but goes up to EL 14, which might challenge your PCs without consulting other sources.
The Manual of the Planes gives a 1 in 20 chance per hour of a a random encounter on the Astral Plane using Table 5-3: Astral Encounters (53), and those range from easy (a CR 5 solitary nightmare (MM 194)) to extreme (the CR 17 astral form of a Wiz17), but centers on EL 11 encounters. Essentially, that means at least once per day, the PCs will encounter something, and it's liable to be ready for a fight (or running from one), and some lousy days on the Astral Plane it's liable to be an encounter traffic jam.
What this also means is that your PCs are leveled appropriately to start adventuring on the Astral Plane. I understand you not wanting them there, but the game thinks it's okay that they are.
Increasing the basic lethality of the Astral Plane is seriously the easiest way to make the players think again about visiting, but you could place a plot hook there so terrifying the PCs can't even imagine dealing with it--a cult of mind flayers attempting to bring back to life a dead god, for example--then say offhandedly, "Yeah, that's for when you hit epic levels."
There Might Be Confusion about Traveling the Astral Plane
The D&D Cosmology says, "All planes... are coexistent with the Astral Plane" (DMG 150), but the Astral Plane lacks the overlap with the Prime Material Plane possessed by, for example, the Ethereal Plane or the Plane of Shadow. Instead the Astral Plane "envelops the whole cosmology like a cloud." A ship or creature on the Astral Plane doesn't have correspondence to any location on the Prime Material Plane; there's just no relationship there.
To clarify, when the ship travels to the Astral Plane, the ship arrives at a destination that's only and ever on the Astral Plane. When the ship returns to Prime Material Plane, the PCs pick a destination at which the ship will arrive, and poof! the ship appears there (although possibly 5d% miles off-target if the repurposing incorporated an effect like the spell plane shift [conj] (PH 262) and you interpret the spell that way). That effect is like a high-volume, time-consuming (two standard actions!), and maybe more accurate version of the spell teleport [conj] (PH 292-3). In a more magic-intensive game, the PCs could've been doing that at least 4 levels ago, albeit on a more limited scale.
Further, if the ship's generating an effect like the spell plane shift [conj] (PH 262), then the ship should arrive 5d% miles from the chosen destination on the Astral Plane, which might not matter if the PCs are just using the Astral Plane as an escape route but does mean every time the ship arrives on the Astral Plane it's in a different place, possibly with new, unknown threats.
Slowing the Ship
Foes tired of the PCs escaping to the Astral Plane can discover their Astral Plane destination with the feat Astral Tracking (Dragon Compendium Volume 1 92) and, once they arrive at that destination, cast on the site the spell hallow [evoc] (PH 238), tying to the site an effect like the spell dimensional anchor [abjur] (PH 221).
Then, to reach a different Astral Plane destination beyond whatever the ship's now-blocked default, the PCs must either learn of another Astral Plane location via research (the resources for which you needn't provide until you're ready for this to be a thing again) or discover that location via exploration, which entails entering the Astral Plane by other means and scooting around until something presents itself.
Also, so you know, if the ship's prevented from returning to the Prime Material Plane, the PCs should quickly learn that "[o]bjects... cannot move in the Astral Plane, though they may be pushed" (MP 47); that might make the crew unhappy. (The 3.5 DMG says the Astral Plane has subjective directional gravity (154) meaning the Astral Plane has "no gravity for unattended objects" (148)--the upper limit of what objects can be attended is up to the DM.) This might mean PCs traveling bodily in the Astral Plane, navigating its hazards and encounters, to reach help sufficient to push their ship, but that A) is an adventure! and B) likely requires abandoning their ship. So you know, only "githyanki possess special item creation feats that enable them to create their famed astral ships" (MP 52). Let hilarity ensue.
A Final Concern
Although the githyanki have astral ships (see above), they are "difficult to create, requiring years of work" (MP 52), and the spell that does what your level 13 characters are doing is similar to the 9th-level Sor/Wiz spell planar navigation [conj] (Sto 119-20) (although that spell transports the ship to a body of water on any plane instead of just to the Astral Plane). I mention this because based on the precedent set by that spell your PCs are doing something similar at least 4 levels early (barring shenanigans) than the game expects, even if it is via a magic item (i.e. their repurposed ship). It might not seem like a lot, but 4 levels is the most extreme difference between a challenging encounter and a very difficult encounter (DMG 49). It appears too late to introduce a wrinkle into the repurposing process that makes their traveling to the Astral Plane expensive, limted, time-consuming, or unreliable, but you might discuss these nuts-and-bolts issues with your group.