My relatively uneducated analysis:
Why a military LASER battery would be worse than using conventional missiles:
1.) My understanding of LASER weapons is that, for even a very large chemically powered LASER battery there is a great deal of refraction as the radiation passes through the atmosphere.
2.) It would have to be very large to produce enough power and thus would be a major target.
3.) It may be very expensive to build relatively speaking.
4.) Targeting would be a major issue. Even very small movements of the LASER at the base of the beam would produce a major shift at the point of impact at a distance.
5.) It may have to concentrate on a single point on the target long enough to cause significant damage.
Why a military LASER battery would be superior to conventional missiles:
1.) One would not be able to tell as easily where the installation was even as it destroyed targets, because the LASER itself would be invisible unlike a conventional missile. It would be difficult to trace its path simply by trying to collect the pattern of light refracted by the particles of the atmosphere it travels through.
2.) Providing energy to the installation, perhaps through underground power lines, would replace having to manufacture missiles. The energy would be converted and directed and turned into a weapon. This is a relatively more effective solution. Once there is an installation, all that is required it to feed it electricity.
3.) It would give Iran a more admirable standing in terms of R&D in the international community, and serve as a greater deterrent to aerial bombing in the first place.
4.) It could be modified to bring down satellites (even given the extra distance the radiation would travel, as one gets to higher altitudes where the density of gasses and particle matter is lower, there is correspondingly less refraction), ballistic missiles, &c.
5.) This is a rather uneducated guess, but I think the expertise to build such an installation would already exists in Iran. It's not so much producing a powerful LASER that is the difficult task but more figuring out a way that it can target reliably. Furthermore, I think directed energy weapons are bound to be the future of many weapons technologies, so by developing these installations Iran would be helping to prepare itself for future defense needs.
Regardless, LASERs are a novel solution. I think Iran should research them because they do and will have many military applications.