These themocouples have a tiny spot weld between two thin wires to make the active sensor element, which results in a very low thermal mass. Hence they change temperature quickly, which is the same thing as reacting to temperature changes quickly. As soon as you mount them in a larger substrate or coating (eg to provide a sterile insulation, to prevent breakage, to electrically isolate) you increase the thermal mass, so you have to wait longer for stabilisation.
I would add a couple of suggestions for the design:
You are using 741 OP-AMP, which is not rail-to-rail, and you're using it for driving the base of a transistor: what happens is that when the output of the 741 is high, it will be at about Vcc - 1V, that is enough to keep the transistor on. I would suggest using a rail-to-rail OPAMP or adding a small resistance to the emitter of the transistor to limit the current when the input is high (could be even better because you mantain the fan at a slower speed but still cooling).
When designing with sensors, such as photoresistors or thermistors, it's better to - first know the value at room temperature of these sensors - and then picking a potentiometer just bigger to simulate the behavior of this sensor, and check that the circuit is working.
UPDATE: from the datasheet, the typical voltage swing is 13-14 V (you can measure the exact maximum value just measuring the positive saturation voltage), and by design the lose in the range tends to be more in the upper rail, because the output stage has a \$ {V_{CE}}^{sat} + {V_{BE}^{ON}} \simeq 0.2 + 0.6 \simeq 0.8 V \$.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
UPDATE 2: Now I see that you are powering your circuit at +12V / 0V, that is NOT the exact supply voltage specified for the 741 OPAMP: it requires a dual-rail, \$ \pm 15V \$ fix this as the first thing.
You can see as your OPAMP is outputting 10 V instead of 12, and 1.2V instead of 0; the first, with the drop over the resistor, makes the transistor always on, as you can see that the base voltage is 11V, enough to keeping it on.
And...why did you use a diode to simulate a fan??? Seems a quite different load.
UPDATE TO THE UPDATE:
I'm glad that it works, at least the simulation: however, you are still using a single rail supply (+12:0, +15:0). The 741 wants +15:-15, so the best thing to do is CHANGING THE OPAMP. It's not expensive at all and you can use a rail-to-rail (again), that is better for single supply applications, down to 3.3V if you need that; or, for your case, +12 or +5.
This is an option, here there is plenty, you have only to choose, based primarily on availability for your purpose. For the simulator, you can also find many options.
Best Answer
Edit: there are a lot of products already on the market exactly like this if you don't want to make it yourself. Look at numbers 2 through 5: http://homecooking.about.com/od/kitchenequipmentreviews/tp/electricthermom.htm
If you can get a resonant coil and thermistor system with enough SNR to reliably detect temperature remotely, then that seems to be the best solution. If not, here's some information about wireless sensor nodes.
In terms of wireless data transmission, infrared radiation of an object increases in proportion with temperature. Unfortunately, this information could only tell us the temperature of the surface of the meat, and not the center. At first I thought maybe you could use a spike with very high thermal conductivity so that you could see the temperature of the inside by looking at the spike with a thermal camera. However, the spike would just effectively cook whatever its touching so it would probably do more harm than good. For this reason, whatever design you choose to go with, the spike you insert should have very low thermal conductivity so that it doesn't cook the meat from the inside. Unless you want that.
The IR radiation coming from the oven/pan also introduces another problem: noise. You will have to select an IR transmitter with a frequency that doesn't overlap with the IR noise from the cooking implements. Maybe all IR transmitters are designed this way anyway, I don't know. Just something to be aware of. You could use an RF transmitter instead, at the cost of higher power. RF has the advantage that it will penetrate through more obstacles than IR.
A thermoelectric generator would be the most effective way to harvest energy. Because there is expected to be a large temperature difference between the outside of the meat, and the insulated inside, you could place a TEG along this gradient. But then you probably need to have a voltage regulator circuit to power your digital control circuit, temperature sensor and transmitter. I don't know if the TEG can produce the power you would need. It may be easier to just use an energy storage element like a super capacitor or chemical battery. Here is a tiny battery that operates up to 85°C: http://www.infinitepowersolutions.com/images/stories/downloads/ips_thinergy_mec225_product_data_sheet_ds1014_v1-1_final_20110913.pdf
They say, "Standard electrochemical degradation is proportional to temperature increase. Contact IPS for performance information regarding higher temperature applications up to 150°C."