Most gods have opposing gods they are superior to, and others they suck against. With Kronos, you own Norse opponents, but Isis will obviously give you a hard time. That does not mean that you do not stand a chance though.
I am no Attie player, but then again, I am a 1750 average (1802 highest), so my general knowledge of the game should still suffice to help you.
Isis has very good defences against a Krush, and a smart Isis player will probably not advance as late as Brtnboarder495 suggested, knowing that this would give the Kronos too much time to attack the unupgraded towers. Priests and pharaohs also benefit greatly from hitting classical age. So he will most likely advance to classical somewhat earlier, and as you already pointed out, he will make several priests in preparation for the Krush. These priests are not free, so all of this will delay his FH to a certain extent.
If I were you, I would try to boom. Do not try the Krush against Isis at all. Instead, research your first econ-ups early and take two more TCs. You can start making the first TC before even hitting classical age. Do not advance at 3:40. In fact, you can go classical at 5:00 for a very fat economy and be fine! Use the additional resources of your strong archaic economy to utilize the Atlantean privilege to erect another TC in archaic age.
Once you have hit classical, make sure to gather information on what he does. Against a Kronos the Isis player might well decide to erect some barracks and go for a classical age army. This is no problem for you - provided you notice in time. So good reconnaissance is of the essence.
If the Isis player goes heroic following the usual Eggy plan, you grasp a third TC and then make barracks and counter-barracks. As Kronos you get myth units cheaper, making additional TCs especially valuable to you, because more TCs mean more favor. Be prepared for priest armies though. Make sure to use the additional TCs to produce citizens in order to gain an economical advantage.
On the other hand, make sure to reduce your citizen production when Isis has hit heroic age, so that you have resources left to quickly make an army and do not keep spending all you have on more citizens. You should now have a very phat economy and plenty of pop space due to three TCs. Now go for a pop-limit army and fight her. Go heroic when your resources allow. Your classical troops allow you to counter all migdol units, which is a specialty of the Atlantean race. Atlantean are weakest against infantry, but infantry is not the strong side of a FH Eggy. Elephants, camels and chariots pose no threat to your katapeltes and turma, especially since you have the greater pop space on your side (which means your army is larger).
Now that you have your pop limit army and are not forgetting about armory upgrades, where to attack her? Well, do not smoke up your troops at heavily defended places. If you can overrun an unguarded enemy TC, fine, but if it is heavily defended, then stay away of it. Remember the Eggy weakness known as "gold". Isis can go FH on her home mine, but that is about it. She will need a remote mine right afterwards (unless she happens to have a second mine in her home base). Keep scouting all remote gold mines! Tower up those that are closest to her! Use several towers per mine, as only one tower cannot defend anything. You should now have the economy to do that. There is still a good likelihood that she can claim one remote mine by placing her first migdol there. Erected by all her gold villies and with the pharaoh empowering the construction site you will hardly be able to prevent that. This allows her to produce heroic units and fight for some time. But Egypt is the most gold-intensive race, and she will need more gold soon. So make (or timeshift) towers at all the other remote mines that are near her base and make sure to send a turma to the other mines now and then so that she does not secretly mine behind your back. This obviously means you must scout the whole map properly, and do so early. Use waypoints for your scouting units to minimize micro effort. If half of your minimap is still black after 10 minutes, you can never hope to keep Isis off gold.Do not attack Isis' food and wood income (unless you stumble over good opportunities to do so). Focus on keeping her off gold. That is what hurts Eggy most. Once you control all free mines, search for that trading route that she has probably resorted to. She may be able to defend a short trading route (half map size or shorter). Do not worry about that; such trading routes are rather inefficient, and for the same pop your citizens are bringing in much more gold. But you definitely need to find and take out any long trading route that she may have. Slay the donkeys, destroy the market, wall up the path, timeshift a palace into the path, do anything but stop that route!!
And if she turtles and goes mythic for a titan?
Well, if everything has gone as described above, you control most of the map and have the better income. So what is wrong with going mythic yourself and make a titan of your own? Egypt is known to be better in mythic age, but that is why you won yourself an edge before the game went there. Defend this edge, starve her off gold and crush her in the end!
Darkness is a state of mind
Valor is the contempt of Death and Pain. (Tacitus)
Problems worthy of attack prove their worth by hitting back. (Piet Hein)