You've just had your inlet manifold cleaned, so if you leave the EGR valve in operation you will start to choke it up again. For that reason alone I'd disable it.
But in addition to that, the EGR valve itself can trigger limp mode, especially when the inlet is full of sticky gunk. Although you have now had it cleaned, disabling the EGR would eliminate this as a point of failure, and if you're lucky, fix the
problem.
My first introduction to limp mode and EGR related failures was with a TDI 90 in a Mk.2
Ibiza. This has a wastegated turbo, so no vanes to stick. It would go into limp mode at motorway overtaking speeds, frustrating and potentially dangerous.
The EGR valve was sticking open, clogged with the sticky sludge resulting from hot sooty exhaust hitting oily crankcase vapours in the inlet charge. EGR is supposed to be closed at low revs, open in the midrange when the engine is loaded (ECU works all this out) and closed again at higher revs. When it fails to close, exhaust leaks past it and causes overpressure in the inlet, and the ECU triggers limp mode.
Disabling the EGR on our cars is really easy, just disconnect one electrical connector, the one to the N18 valve. Five minutes the first time you do it (find the right connector, work out how the damned things unlock, tie the loose end out of the way, wrap with duct tape to protect against dirt). Thirty seconds to reconnect for servicing. The valve is easy to find at the back of the engine bay.
Downsides to disconnecting it. Well, the engine will now reach higher peak combustion temperatures, during the transient conditions that produce them, and generate a little NOx. The exhaust will be a little hotter during those times, so the turbine stage will get hotter. However, I think the temperatures are well within the allowable range for the engine components as I think the earliest TDI's had no EGR, California's paranoia having not reached out so far.
If you're worried about pollution, you will have modified the car out of compliance with one parameter, the NOx emissions. In the regulatory sense, this is not a
problem as NOx is not tested at MOT time and is only regulated on the engines as manufactured. However, if a dealer notices it during service they will reconnect the EGR - they are obliged to, I think.
To counter this, EGR is the main reason that diesels still produce smoke - the ECU is able to control combustion well enough over most areas of operation to keep smoke generation at a minimum. So the use of EGR to regulate NOx results in an increase in particulate generation, another pollutant that is regulated.
There are many studies that point a finger at NOx as a smog precursor and ozone-depleter. I don't pretend to have read them all or be an expert, but what I've seen convinces me that the case is far from clear-cut and that NOx regulation on its own may well be counter-productive, allowing other pollutants to make the situation worse.
(boring bit follows)
Ozone formation at ground level is driven by NOx and VOC (Volatile Organic Compound) levels.
The principal source of reactive VOCs in the U.S. is the natural emission of isoprene from hardwood forests.
http://www.heartland.org/policybot/results/18973/EPA_Rule_Is_Making_Ozone_Smog_Worse.html
http://www-personal.umich.edu/~sillman/ozone.htm
http://books.nap.edu/openbook.php?record_id=1889&page=211
There is a case that NOx control is inappropriate, and that ozone formation is mainly due to the presence of low level of NOx in association with high levels of VOC's (in automotive terms, fuel and oil vapours). The obvious corollary is that NOx control is inappropriate (whether on motor vehicles or the biggest NOx generators, power plants) and that more attention should be paid to VOC control. Higher levels of NOx actually decrease ozone by a catalytic reaction.
http://books.nap.edu/openbook.php?record_id=1889&page=351